home *** CD-ROM | disk | FTP | other *** search
open in:
MacOS 8.1
|
Win98
|
DOS
view JSON data
|
view as text
This file was processed as: ArcFS Archive
(archive/arcFS).
You can browse this item here: rasmol
Confidence | Program | Detection | Match Type | Support
|
---|
100%
| dexvert
| ArcFS Archive (archive/arcFS)
| magic
| Supported |
100%
| file
| RISC OS archive (ArcFS format)
| default
| |
99%
| file
| data
| default
| |
100%
| TrID
| Acorn ArcFS Archive
| default
| |
100%
| gt2
| Kopftext: 'Archive'
| default (weak)
| |
100%
| detectItEasy
| Archive: ArcFS
| default
|
|
hex view+--------+-------------------------+-------------------------+--------+--------+
|00000000| 41 72 63 68 69 76 65 00 | 14 04 00 00 24 06 00 00 |Archive.|....$...|
|00000010| 28 00 00 00 64 00 00 00 | 00 00 00 00 00 00 00 00 |(...d...|........|
|00000020| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000030| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000040| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000050| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000060| 82 21 52 61 73 4d 6f 6c | 00 00 00 00 ff ff ff ff |.!RasMol|........|
|00000070| 46 dc fd ff 39 7b 03 ff | 30 00 00 00 ff ff ff ff |F...9{..|0.......|
|00000080| 40 02 00 80 82 21 42 6f | 6f 74 00 00 00 00 00 00 |@....!Bo|ot......|
|00000090| b8 01 00 00 46 eb ff ff | 6d d3 8b a0 03 00 57 3a |....F...|m.....W:|
|000000a0| b8 01 00 00 c1 06 00 00 | 82 21 48 65 6c 70 00 00 |........|.!Help..|
|000000b0| 00 00 00 00 b6 5f 00 00 | 47 ff ff ff fb b2 c8 00 |....._..|G.......|
|000000c0| 03 00 6e c7 b6 5f 00 00 | 9d 08 00 00 82 21 52 75 |..n.._..|.....!Ru|
|000000d0| 6e 00 00 00 00 00 00 00 | ef 02 00 00 46 eb ff ff |n.......|....F...|
|000000e0| c4 5a 04 ff 03 00 63 ff | ef 02 00 00 77 68 00 00 |.Z....c.|....wh..|
|000000f0| 82 21 52 75 6e 49 6d 61 | 67 65 00 00 af 40 02 00 |.!RunIma|ge...@..|
|00000100| 47 f8 ff ff db 7c c8 00 | 03 00 d1 69 af 40 02 00 |G....|..|...i.@..|
|00000110| 8a 6b 00 00 82 21 53 70 | 72 69 74 65 73 00 00 00 |.k...!Sp|rites...|
|00000120| 6c 18 00 00 46 f9 ff ff | a2 db cc aa 03 00 4a 24 |l...F...|......J$|
|00000130| 6c 18 00 00 5d ac 02 00 | 82 43 68 6f 69 63 65 73 |l...]...|.Choices|
|00000140| 00 00 00 00 11 00 00 00 | 46 fd ff ff a7 5c fa a3 |........|F....\..|
|00000150| 03 00 8e fa 11 00 00 00 | ed c4 02 00 82 44 6f 63 |........|.....Doc|
|00000160| 73 00 00 00 00 00 00 00 | ff ff ff ff 46 dc fd ff |s.......|....F...|
|00000170| ca 80 03 ff 00 00 00 00 | ff ff ff ff 8c 01 00 80 |........|........|
|00000180| 82 32 36 62 65 74 61 31 | 00 00 00 00 25 3e 00 00 |.26beta1|....%>..|
|00000190| 47 ff ff ff a5 bc c6 00 | 03 00 13 c9 25 3e 00 00 |G.......|....%>..|
|000001a0| 22 c5 02 00 82 32 36 62 | 65 74 61 32 00 00 00 00 |"....26b|eta2....|
|000001b0| 17 10 00 00 47 ff ff ff | 5b 40 0d 00 03 00 b1 2a |....G...|[@.....*|
|000001c0| 17 10 00 00 6b 03 03 00 | 00 21 52 65 61 64 4d 65 |....k...|.!ReadMe|
|000001d0| 00 00 00 00 79 06 00 00 | 47 ff ff ff 70 de c8 00 |....y...|G...p...|
|000001e0| 33 0c 98 ac 68 04 00 00 | 24 00 00 00 82 48 65 6c |3...h...|$....Hel|
|000001f0| 70 46 69 6c 65 00 00 00 | 27 19 01 00 46 ff ff ff |pFile...|'...F...|
|00000200| ca e7 24 a9 03 00 de b5 | 27 19 01 00 a6 13 03 00 |..$.....|'.......|
|00000210| 82 4d 65 73 73 61 67 65 | 73 00 00 00 48 04 00 00 |.Message|s...H...|
|00000220| 46 ff ff ff 09 de c9 aa | 03 00 d0 c4 48 04 00 00 |F.......|....H...|
|00000230| f1 2c 04 00 82 53 70 72 | 69 74 65 73 00 00 00 00 |.,...Spr|ites....|
|00000240| 78 35 00 00 46 f9 ff ff | 30 d1 cc aa 03 00 d6 1b |x5..F...|0.......|
|00000250| 78 35 00 00 5d 31 04 00 | 82 54 65 6d 70 6c 61 74 |x5..]1..|.Templat|
|00000260| 65 73 00 00 c3 19 00 00 | 46 ec ff ff 4c 6f c9 aa |es......|F...Lo..|
|00000270| 03 00 66 17 c3 19 00 00 | f9 66 04 00 00 00 00 00 |..f.....|.f......|
|00000280| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000290| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|000002a0| 82 21 52 65 61 64 4d 65 | 00 00 00 00 79 06 00 00 |.!ReadMe|....y...|
|000002b0| 47 ff ff ff 70 de c8 00 | 33 00 98 ac 79 06 00 00 |G...p...|3...y...|
|000002c0| 24 00 00 00 82 64 61 74 | 61 00 00 00 00 00 00 00 |$....dat|a.......|
|000002d0| ff ff ff ff 46 dc fd ff | 8d 82 03 ff 30 00 00 00 |....F...|....0...|
|000002e0| ff ff ff ff f0 03 00 80 | 82 31 63 72 6e 00 00 00 |........|.1crn...|
|000002f0| 0e 00 00 00 ca 86 00 00 | 46 2a f1 ff 5f da 38 9a |........|F*.._.8.|
|00000300| 03 00 0c dd ca 86 00 00 | e0 80 04 00 82 33 63 72 |........|.....3cr|
|00000310| 6f 00 00 00 0e 00 00 00 | 9f 82 02 00 46 2a f1 ff |o.......|....F*..|
|00000320| a6 da 38 9a 03 00 9d bf | 9f 82 02 00 ce 07 05 00 |..8.....|........|
|00000330| 82 61 73 70 69 72 69 6e | 00 00 00 00 cf 06 00 00 |.aspirin|........|
|00000340| 46 29 f1 ff 54 32 5d 99 | 33 00 54 cf cf 06 00 00 |F)..T2].|3.T.....|
|00000350| 91 8a 07 00 82 61 74 72 | 6f 70 69 6e 65 00 00 00 |.....atr|opine...|
|00000360| 49 0d 00 00 46 29 f1 ff | ac 34 5d 99 33 00 63 e9 |I...F)..|.4].3.c.|
|00000370| 49 0d 00 00 84 91 07 00 | 82 62 75 63 6b 79 00 00 |I.......|.bucky..|
|00000380| 0e 00 00 00 d7 0f 00 00 | 46 2a f1 ff f7 6a 5f a1 |........|F*...j_.|
|00000390| 03 00 6a 0c d7 0f 00 00 | f1 9e 07 00 82 63 61 66 |..j.....|.....caf|
|000003a0| 66 65 69 6e 65 00 00 00 | a6 08 00 00 46 29 f1 ff |feine...|....F)..|
|000003b0| ec 3a 5d 99 33 00 03 e7 | a6 08 00 00 ec ae 07 00 |.:].3...|........|
|000003c0| 82 52 6f 74 61 74 65 00 | 0e 00 00 00 ac 00 00 00 |.Rotate.|........|
|000003d0| 46 2b f1 ff d3 ca 89 b8 | 03 00 48 91 ac 00 00 00 |F+......|..H.....|
|000003e0| b6 b7 07 00 82 53 63 72 | 69 70 74 31 00 00 00 00 |.....Scr|ipt1....|
|000003f0| 8d 02 00 00 46 2b f1 ff | d3 90 8a b8 03 00 c7 0e |....F+..|........|
|00000400| 8d 02 00 00 86 b8 07 00 | 82 53 63 72 69 70 74 32 |........|.Script2|
|00000410| 00 00 00 00 16 03 00 00 | 46 2b f1 ff 66 82 8a b8 |........|F+..f...|
|00000420| 03 00 e0 f6 16 03 00 00 | 37 bb 07 00 00 0d 00 00 |........|7.......|
|00000430| 00 00 00 00 0e 00 00 00 | 00 00 00 00 cc fe ff ff |........|........|
|00000440| 18 00 00 00 f8 fe ff ff | 38 00 0e 07 ac 09 00 00 |........|8.......|
|00000450| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000460| 00 00 00 00 00 00 00 00 | 00 00 00 00 00 00 00 00 |........|........|
|00000470| 00 00 00 00 64 8e 26 25 | ea 14 6a 57 97 75 b0 ba |....d.&%|..jW.u..|
|00000480| bc 29 76 b3 82 ec 6f 8c | 5a 9d c3 02 84 9b 3a 63 |.)v...o.|Z.....:c|
|00000490| 18 ab 0e 73 9a 8c 72 f0 | 20 cc d1 06 56 06 35 c7 |...s..r.| ...V.5.|
|000004a0| d8 18 d0 c1 e6 18 64 20 | c0 b7 5d 77 ca 49 26 de |......d |..]w.I&.|
|000004b0| 4d 0a 90 e1 d2 4c 8a d5 | 67 14 7f 2d b9 71 06 4c |M....L..|g..-.q.L|
|000004c0| 00 1a 26 5c 75 99 8d 55 | 16 1c 75 88 41 93 4d 25 |..&\u..U|..u.A.M%|
|000004d0| 82 10 47 7a 34 d1 31 98 | 64 61 18 36 07 71 0a 18 |..Gz4.1.|da.6.q..|
|000004e0| 41 9e 19 ae 75 26 c7 5b | 6e 98 41 d4 80 2d 86 21 |A...u&.[|n.A..-.!|
|000004f0| c6 1b 75 e4 65 1c 5a 20 | 22 d5 99 44 14 59 84 51 |..u.e.Z |"..D.Y.Q|
|00000500| 83 44 e5 c5 1b 1c ba e1 | 84 60 74 72 b0 a0 c0 1c |.D......|.`tr....|
|00000510| 65 44 f5 e4 09 21 20 51 | 06 1b 70 9c 90 54 1a 8c |eD...! Q|..p..T..|
|00000520| 01 19 56 78 e5 45 45 e6 | 92 05 a9 69 e1 6b 63 d0 |..Vx.EE.|...i.kc.|
|00000530| 41 54 1e 0b 9a 37 06 53 | 03 02 48 93 70 c9 29 50 |AT...7.S|..H.p.)P|
|00000540| 06 1e 18 5a 25 1e 6f 4f | a6 d6 e6 09 66 a2 69 04 |...Z%.oO|....f.i.|
|00000550| 9b 65 a8 39 5f 1a 70 8e | 19 02 9d 6c d8 99 06 9e |.e.9_.p.|...l....|
|00000560| 7a ca c1 27 08 46 b0 46 | 87 6b b0 29 e0 dd 52 64 |z..'.F.F|.k.)..Rd|
|00000570| e0 27 de 1d 69 3c d5 d5 | 57 61 69 86 90 6d ba 45 |.'..i<..|Wai..m.E|
|00000580| 15 de 1c 63 d8 b5 10 52 | 8c 9a f7 1a 63 02 45 e5 |...c...R|....c.E.|
|00000590| 46 7c b0 81 70 82 0c 0a | 31 14 46 0c 27 28 10 06 |F|..p...|1.F.'(..|
|000005a0| 80 cb 36 db 90 0c 96 ee | 34 26 11 6f 8c 31 87 a7 |..6.....|4&.o.1..|
|000005b0| a0 ee e9 26 a6 72 6e 7a | 56 9d 38 32 78 a7 69 a1 |...&.rnz|V.82x.i.|
|000005c0| 0e 76 02 19 37 85 a1 e6 | 9f 6e 34 34 5f 80 4c 45 |.v..7...|.n44_.LE|
|000005d0| 35 07 77 94 31 e7 dc 96 | c9 4e 8b 14 af 76 c1 41 |5.w.1...|.N...v.A|
|000005e0| c7 8d ca c6 d0 ab 1b d1 | 0a ac ec 0c bd be a1 66 |........|.......f|
|000005f0| ae 4e dd f1 46 83 4b c9 | e7 c6 4b 4a 31 15 27 08 |.N..F.K.|..KJ1.'.|
|00000600| 42 2c f5 c6 1a 3d 79 b5 | 13 14 19 97 c1 1b 11 f1 |B,...=y.|........|
|00000610| 8a 31 ed 1a 5e 9e 20 10 | 1c 9f 5a 75 42 7d 32 d3 |.1..^. .|..ZuB}2.|
|00000620| b1 14 cd c2 46 69 6c 65 | 44 61 74 61 82 21 52 65 |....File|Data.!Re|
|00000630| 61 64 4d 65 00 00 00 00 | 79 06 00 00 47 ff ff ff |adMe....|y...G...|
|00000640| 70 de c8 00 03 00 98 ac | 52 61 73 4d 6f 6c 20 32 |p.......|RasMol 2|
|00000650| 2e 36 62 65 74 61 32 20 | 2f 20 52 49 53 43 20 4f |.6beta2 |/ RISC O|
|00000660| 53 20 31 2e 32 30 20 28 | 32 30 2d 41 75 67 2d 39 |S 1.20 (|20-Aug-9|
|00000670| 36 29 0a 0a 54 68 69 73 | 20 61 70 70 6c 69 63 61 |6)..This| applica|
|00000680| 74 69 6f 6e 20 68 61 73 | 20 62 65 65 6e 20 70 6f |tion has| been po|
|00000690| 72 74 65 64 20 66 72 6f | 6d 20 74 68 65 20 6f 72 |rted fro|m the or|
|000006a0| 69 67 69 6e 61 6c 20 58 | 31 31 20 76 65 72 73 69 |iginal X|11 versi|
|000006b0| 6f 6e 20 6f 66 20 52 61 | 73 4d 6f 6c 0a 77 68 69 |on of Ra|sMol.whi|
|000006c0| 63 68 20 69 73 20 43 6f | 70 79 72 69 67 68 74 20 |ch is Co|pyright |
|000006d0| a9 20 31 39 39 32 2d 39 | 34 20 62 79 20 52 6f 67 |. 1992-9|4 by Rog|
|000006e0| 65 72 20 53 61 79 6c 65 | 2e 20 54 68 65 20 69 6d |er Sayle|. The im|
|000006f0| 70 6c 65 6d 65 6e 74 61 | 74 69 6f 6e 20 6f 66 20 |plementa|tion of |
|00000700| 74 68 65 0a 52 49 53 43 | 20 4f 53 20 73 70 65 63 |the.RISC| OS spec|
|00000710| 69 66 69 63 20 66 65 61 | 74 75 72 65 73 20 69 73 |ific fea|tures is|
|00000720| 20 a9 20 31 39 39 36 20 | 62 79 20 4d 61 72 74 69 | . 1996 |by Marti|
|00000730| 6e 20 57 fc 72 74 68 6e | 65 72 2e 0a 0a 52 61 73 |n W.rthn|er...Ras|
|00000740| 4d 6f 6c 20 69 73 20 61 | 20 6d 6f 6c 65 63 75 6c |Mol is a| molecul|
|00000750| 61 72 20 67 72 61 70 68 | 69 63 73 20 70 72 6f 67 |ar graph|ics prog|
|00000760| 72 61 6d 20 69 6e 74 65 | 6e 64 65 64 20 66 6f 72 |ram inte|nded for|
|00000770| 20 74 68 65 20 76 69 73 | 75 61 6c 69 73 61 74 69 | the vis|ualisati|
|00000780| 6f 6e 20 6f 66 0a 70 72 | 6f 74 65 69 6e 73 2c 20 |on of.pr|oteins, |
|00000790| 6e 75 63 6c 65 69 63 20 | 61 63 69 64 73 20 61 6e |nucleic |acids an|
|000007a0| 64 20 73 6d 61 6c 6c 20 | 6d 6f 6c 65 63 75 6c 65 |d small |molecule|
|000007b0| 73 2e 20 54 68 65 20 70 | 72 6f 67 72 61 6d 20 69 |s. The p|rogram i|
|000007c0| 73 20 61 69 6d 65 64 20 | 61 74 0a 64 69 73 70 6c |s aimed |at.displ|
|000007d0| 61 79 2c 20 74 65 61 63 | 68 69 6e 67 20 61 6e 64 |ay, teac|hing and|
|000007e0| 20 67 65 6e 65 72 61 74 | 69 6f 6e 20 6f 66 20 70 | generat|ion of p|
|000007f0| 75 62 6c 69 63 61 74 69 | 6f 6e 20 71 75 61 6c 69 |ublicati|on quali|
|00000800| 74 79 20 69 6d 61 67 65 | 73 2e 0a 0a 46 6f 72 20 |ty image|s...For |
|00000810| 66 75 72 74 68 65 72 20 | 69 6e 66 6f 72 6d 61 74 |further |informat|
|00000820| 69 6f 6e 20 61 62 6f 75 | 74 20 52 61 73 4d 6f 6c |ion abou|t RasMol|
|00000830| 20 61 6e 64 20 74 68 65 | 20 52 49 53 43 20 4f 53 | and the| RISC OS|
|00000840| 20 70 6f 72 74 20 69 6e | 20 70 61 72 74 69 63 75 | port in| particu|
|00000850| 6c 61 72 2c 0a 73 65 65 | 20 74 68 65 20 27 21 48 |lar,.see| the '!H|
|00000860| 65 6c 70 27 20 66 69 6c | 65 20 69 6e 73 69 64 65 |elp' fil|e inside|
|00000870| 20 74 68 65 20 27 21 52 | 61 73 4d 6f 6c 27 20 64 | the '!R|asMol' d|
|00000880| 69 72 65 63 74 6f 72 79 | 2e 20 54 68 65 20 63 6f |irectory|. The co|
|00000890| 6d 6d 61 6e 64 20 6c 69 | 6e 65 20 69 73 0a 65 78 |mmand li|ne is.ex|
|000008a0| 70 6c 61 69 6e 65 64 20 | 69 6e 20 74 68 65 20 66 |plained |in the f|
|000008b0| 69 6c 65 20 27 48 65 6c | 70 46 69 6c 65 27 20 69 |ile 'Hel|pFile' i|
|000008c0| 6e 73 69 64 65 20 74 68 | 65 20 27 21 52 61 73 4d |nside th|e '!RasM|
|000008d0| 6f 6c 27 20 64 69 72 65 | 63 74 6f 72 79 2e 20 46 |ol' dire|ctory. F|
|000008e0| 65 61 74 75 72 65 73 0a | 69 6e 74 72 6f 64 75 63 |eatures.|introduc|
|000008f0| 65 64 20 77 69 74 68 20 | 76 65 72 73 69 6f 6e 20 |ed with |version |
|00000900| 32 2e 36 20 61 72 65 20 | 64 65 73 63 72 69 62 65 |2.6 are |describe|
|00000910| 64 20 69 6e 20 74 68 65 | 20 72 65 6c 65 61 73 65 |d in the| release|
|00000920| 20 6e 6f 74 65 73 20 27 | 32 36 62 65 74 61 31 27 | notes '|26beta1'|
|00000930| 0a 61 6e 64 20 27 32 36 | 62 65 74 61 32 27 20 69 |.and '26|beta2' i|
|00000940| 6e 20 74 68 65 20 27 44 | 6f 63 73 27 20 64 69 72 |n the 'D|ocs' dir|
|00000950| 65 63 74 6f 72 79 20 69 | 6e 73 69 64 65 20 27 21 |ectory i|nside '!|
|00000960| 52 61 73 4d 6f 6c 27 2e | 0a 0a 54 68 65 20 64 69 |RasMol'.|..The di|
|00000970| 72 65 63 74 6f 72 79 20 | 27 64 61 74 61 27 20 63 |rectory |'data' c|
|00000980| 6f 6e 74 61 69 6e 73 20 | 73 6f 6d 65 20 73 61 6d |ontains |some sam|
|00000990| 70 6c 65 20 6d 6f 6c 65 | 63 75 6c 65 73 20 61 6e |ple mole|cules an|
|000009a0| 64 20 73 63 72 69 70 74 | 73 2e 20 27 31 63 72 6e |d script|s. '1crn|
|000009b0| 27 0a 61 6e 64 20 27 33 | 63 72 6f 27 20 61 72 65 |'.and '3|cro' are|
|000009c0| 20 74 77 6f 20 70 72 6f | 74 65 69 6e 73 20 66 72 | two pro|teins fr|
|000009d0| 6f 6d 20 74 68 65 20 42 | 72 6f 6f 6b 68 61 76 65 |om the B|rookhave|
|000009e0| 6e 20 50 72 6f 74 65 69 | 6e 20 44 61 74 61 62 61 |n Protei|n Databa|
|000009f0| 6e 6b 2c 0a 27 61 73 70 | 69 72 69 6e 27 2c 20 27 |nk,.'asp|irin', '|
|00000a00| 61 74 72 6f 70 69 6e 65 | 27 20 61 6e 64 20 27 63 |atropine|' and 'c|
|00000a10| 61 66 66 65 69 6e 65 27 | 20 61 72 65 20 41 6c 63 |affeine'| are Alc|
|00000a20| 68 65 6d 79 20 66 69 6c | 65 73 2e 0a 0a 27 53 63 |hemy fil|es...'Sc|
|00000a30| 72 69 70 74 31 27 20 64 | 69 73 70 6c 61 79 73 20 |ript1' d|isplays |
|00000a40| 74 68 65 20 31 63 72 6e | 20 6d 6f 6c 65 63 75 6c |the 1crn| molecul|
|00000a50| 65 20 69 6e 20 61 20 73 | 70 61 63 65 20 66 69 6c |e in a s|pace fil|
|00000a60| 6c 69 6e 67 20 72 65 70 | 72 65 73 65 6e 74 61 74 |ling rep|resentat|
|00000a70| 69 6f 6e 0a 77 69 74 68 | 20 73 70 65 63 75 6c 61 |ion.with| specula|
|00000a80| 72 20 68 69 67 68 6c 69 | 67 68 74 73 2e 20 27 53 |r highli|ghts. 'S|
|00000a90| 63 72 69 70 74 32 27 20 | 64 69 73 70 6c 61 79 73 |cript2' |displays|
|00000aa0| 20 74 68 65 20 61 73 70 | 69 72 69 6e 20 6d 6f 6c | the asp|irin mol|
|00000ab0| 65 63 75 6c 65 20 75 73 | 69 6e 67 0a 6d 6f 72 65 |ecule us|ing.more|
|00000ac0| 20 61 64 76 61 6e 63 65 | 64 20 66 65 61 74 75 72 | advance|d featur|
|00000ad0| 65 73 20 65 2e 67 2e 20 | 64 69 73 70 6c 61 79 69 |es e.g. |displayi|
|00000ae0| 6e 67 20 74 68 65 20 56 | 61 6e 20 64 65 72 20 57 |ng the V|an der W|
|00000af0| 61 61 6c 73 20 64 6f 74 | 20 73 75 72 66 61 63 65 |aals dot| surface|
|00000b00| 20 61 6e 64 0a 61 74 6f | 6d 20 6c 61 62 65 6c 6c | and.ato|m labell|
|00000b10| 69 6e 67 2e 0a 0a 54 68 | 65 20 73 63 72 69 70 74 |ing...Th|e script|
|00000b20| 20 27 52 6f 74 61 74 65 | 27 20 72 6f 74 61 74 65 | 'Rotate|' rotate|
|00000b30| 73 20 74 68 65 20 63 75 | 72 72 65 6e 74 6c 79 20 |s the cu|rrently |
|00000b40| 6c 6f 61 64 65 64 20 6d | 6f 6c 65 75 63 6c 65 20 |loaded m|oleucle |
|00000b50| 62 79 20 39 30 20 64 65 | 67 72 65 65 73 0a 69 6e |by 90 de|grees.in|
|00000b60| 20 73 74 65 70 73 20 6f | 66 20 31 30 20 64 65 67 | steps o|f 10 deg|
|00000b70| 72 65 65 73 2e 0a 0a 50 | 6c 65 61 73 65 20 64 69 |rees...P|lease di|
|00000b80| 72 65 63 74 20 61 6e 79 | 20 63 6f 6d 6d 65 6e 74 |rect any| comment|
|00000b90| 73 20 61 62 6f 75 74 20 | 74 68 65 20 52 49 53 43 |s about |the RISC|
|00000ba0| 20 4f 53 20 76 65 72 73 | 69 6f 6e 20 74 6f 20 6d | OS vers|ion to m|
|00000bb0| 65 3a 0a 20 20 4d 61 72 | 74 69 6e 20 57 75 65 72 |e:. Mar|tin Wuer|
|00000bc0| 74 68 6e 65 72 0a 20 20 | 4a 61 68 6e 73 74 72 61 |thner. |Jahnstra|
|00000bd0| 73 73 65 20 31 38 0a 20 | 20 37 31 31 31 36 20 47 |sse 18. | 71116 G|
|00000be0| 61 65 72 74 72 69 6e 67 | 65 6e 0a 20 20 47 65 72 |aertring|en. Ger|
|00000bf0| 6d 61 6e 79 0a 20 20 77 | 75 65 72 74 68 6e 65 40 |many. w|uerthne@|
|00000c00| 74 72 69 63 6b 2e 69 6e | 66 6f 72 6d 61 74 69 6b |trick.in|formatik|
|00000c10| 2e 75 6e 69 2d 73 74 75 | 74 74 67 61 72 74 2e 64 |.uni-stu|ttgart.d|
|00000c20| 65 0a 0a 50 6c 65 61 73 | 65 20 64 69 72 65 63 74 |e..Pleas|e direct|
|00000c30| 20 61 6e 79 20 6e 6f 6e | 2d 52 49 53 43 20 4f 53 | any non|-RISC OS|
|00000c40| 2d 73 70 65 63 69 66 69 | 63 20 63 6f 6d 6d 65 6e |-specifi|c commen|
|00000c50| 74 73 20 61 62 6f 75 74 | 20 74 68 65 20 70 72 6f |ts about| the pro|
|00000c60| 67 72 61 6d 20 74 6f 0a | 52 6f 67 65 72 20 53 61 |gram to.|Roger Sa|
|00000c70| 79 6c 65 2c 20 62 65 63 | 61 75 73 65 20 68 65 20 |yle, bec|ause he |
|00000c80| 72 65 61 6c 6c 79 20 77 | 72 6f 74 65 20 74 68 65 |really w|rote the|
|00000c90| 20 77 68 6f 6c 65 20 74 | 68 69 6e 67 3a 0a 20 20 | whole t|hing:. |
|00000ca0| 52 6f 67 65 72 20 53 61 | 79 6c 65 0a 20 20 72 61 |Roger Sa|yle. ra|
|00000cb0| 73 33 32 34 32 35 40 67 | 67 72 2e 63 6f 2e 75 6b |s32425@g|gr.co.uk|
|00000cc0| 0a 46 69 6c 65 44 61 74 | 61 82 21 42 6f 6f 74 00 |.FileDat|a.!Boot.|
|00000cd0| 00 00 00 00 00 b8 01 00 | 00 46 eb ff ff 6d d3 8b |........|.F...m..|
|00000ce0| a0 03 00 57 3a 53 65 74 | 20 52 61 73 4d 6f 6c 24 |...W:Set| RasMol$|
|00000cf0| 44 69 72 20 3c 4f 62 65 | 79 24 44 69 72 3e 0a 49 |Dir <Obe|y$Dir>.I|
|00000d00| 63 6f 6e 53 70 72 69 74 | 65 73 20 3c 52 61 73 4d |conSprit|es <RasM|
|00000d10| 6f 6c 24 44 69 72 3e 2e | 21 53 70 72 69 74 65 73 |ol$Dir>.|!Sprites|
|00000d20| 0a 53 65 74 20 46 69 6c | 65 24 54 79 70 65 5f 31 |.Set Fil|e$Type_1|
|00000d30| 32 42 20 52 61 73 4d 6f | 6c 53 63 0a 53 65 74 20 |2B RasMo|lSc.Set |
|00000d40| 46 69 6c 65 24 54 79 70 | 65 5f 31 32 41 20 50 44 |File$Typ|e_12A PD|
|00000d50| 42 0a 53 65 74 20 46 69 | 6c 65 24 54 79 70 65 5f |B.Set Fi|le$Type_|
|00000d60| 31 32 39 20 41 6c 63 68 | 65 6d 79 0a 53 65 74 20 |129 Alch|emy.Set |
|00000d70| 46 69 6c 65 24 54 79 70 | 65 5f 31 32 38 20 4d 4f |File$Typ|e_128 MO|
|00000d80| 4c 0a 53 65 74 20 46 69 | 6c 65 24 54 79 70 65 5f |L.Set Fi|le$Type_|
|00000d90| 31 32 37 20 4d 4f 50 41 | 43 0a 53 65 74 20 41 6c |127 MOPA|C.Set Al|
|00000da0| 69 61 73 24 40 52 75 6e | 54 79 70 65 5f 31 32 42 |ias$@Run|Type_12B|
|00000db0| 20 2f 3c 52 61 73 4d 6f | 6c 24 44 69 72 3e 2e 21 | /<RasMo|l$Dir>.!|
|00000dc0| 52 75 6e 49 6d 61 67 65 | 20 25 25 2a 30 0a 53 65 |RunImage| %%*0.Se|
|00000dd0| 74 20 41 6c 69 61 73 24 | 40 52 75 6e 54 79 70 65 |t Alias$|@RunType|
|00000de0| 5f 31 32 41 20 2f 3c 52 | 61 73 4d 6f 6c 24 44 69 |_12A /<R|asMol$Di|
|00000df0| 72 3e 2e 21 52 75 6e 49 | 6d 61 67 65 20 25 25 2a |r>.!RunI|mage %%*|
|00000e00| 30 0a 53 65 74 20 41 6c | 69 61 73 24 40 52 75 6e |0.Set Al|ias$@Run|
|00000e10| 54 79 70 65 5f 31 32 39 | 20 2f 3c 52 61 73 4d 6f |Type_129| /<RasMo|
|00000e20| 6c 24 44 69 72 3e 2e 21 | 52 75 6e 49 6d 61 67 65 |l$Dir>.!|RunImage|
|00000e30| 20 25 25 2a 30 0a 53 65 | 74 20 41 6c 69 61 73 24 | %%*0.Se|t Alias$|
|00000e40| 40 52 75 6e 54 79 70 65 | 5f 31 32 38 20 2f 3c 52 |@RunType|_128 /<R|
|00000e50| 61 73 4d 6f 6c 24 44 69 | 72 3e 2e 21 52 75 6e 49 |asMol$Di|r>.!RunI|
|00000e60| 6d 61 67 65 20 25 25 2a | 30 0a 53 65 74 20 41 6c |mage %%*|0.Set Al|
|00000e70| 69 61 73 24 40 52 75 6e | 54 79 70 65 5f 31 32 37 |ias$@Run|Type_127|
|00000e80| 20 2f 3c 52 61 73 4d 6f | 6c 24 44 69 72 3e 2e 21 | /<RasMo|l$Dir>.!|
|00000e90| 52 75 6e 49 6d 61 67 65 | 20 25 25 2a 30 46 69 6c |RunImage| %%*0Fil|
|00000ea0| 65 44 61 74 61 82 21 48 | 65 6c 70 00 00 00 00 00 |eData.!H|elp.....|
|00000eb0| 00 b6 5f 00 00 47 fd ff | ff a1 51 95 1e 03 00 6e |.._..G..|..Q....n|
|00000ec0| c7 52 61 73 4d 6f 6c 20 | 32 2e 36 62 65 74 61 32 |.RasMol |2.6beta2|
|00000ed0| 20 2f 20 31 2e 32 30 20 | 28 32 30 2d 41 75 67 2d | / 1.20 |(20-Aug-|
|00000ee0| 39 36 29 0a 0a 50 75 72 | 70 6f 73 65 3a 20 20 20 |96)..Pur|pose: |
|00000ef0| 20 20 20 4d 6f 6c 65 63 | 75 6c 61 72 20 47 72 61 | Molec|ular Gra|
|00000f00| 70 68 69 63 73 20 56 69 | 73 75 61 6c 69 73 65 72 |phics Vi|sualiser|
|00000f10| 0a 41 75 74 68 6f 72 3a | 20 20 20 20 20 20 20 52 |.Author:| R|
|00000f20| 6f 67 65 72 20 53 61 79 | 6c 65 20 28 72 61 73 33 |oger Say|le (ras3|
|00000f30| 32 34 32 35 40 67 67 72 | 2e 63 6f 2e 75 6b 29 0a |2425@ggr|.co.uk).|
|00000f40| 52 49 53 43 20 4f 53 20 | 70 6f 72 74 3a 20 4d 61 |RISC OS |port: Ma|
|00000f50| 72 74 69 6e 20 57 fc 72 | 74 68 6e 65 72 20 28 77 |rtin W.r|thner (w|
|00000f60| 75 65 72 74 68 6e 65 40 | 74 72 69 63 6b 2e 69 6e |uerthne@|trick.in|
|00000f70| 66 6f 72 6d 61 74 69 6b | 2e 75 6e 69 2d 73 74 75 |formatik|.uni-stu|
|00000f80| 74 74 67 61 72 74 2e 64 | 65 29 0a 52 75 6e 73 20 |ttgart.d|e).Runs |
|00000f90| 75 6e 64 65 72 3a 20 20 | 20 52 49 53 43 20 4f 53 |under: | RISC OS|
|00000fa0| 20 33 2e 31 20 6f 72 20 | 68 69 67 68 65 72 2c 20 | 3.1 or |higher, |
|00000fb0| 73 75 70 70 6f 72 74 73 | 20 52 49 53 43 20 4f 53 |supports| RISC OS|
|00000fc0| 20 33 2e 35 2b 20 74 72 | 75 65 20 63 6f 6c 6f 75 | 3.5+ tr|ue colou|
|00000fd0| 72 20 6d 6f 64 65 73 0a | 20 20 20 20 20 20 20 20 |r modes.| |
|00000fe0| 20 20 20 20 20 20 56 65 | 72 73 69 6f 6e 20 31 2e | Ve|rsion 1.|
|00000ff0| 31 30 20 68 61 73 20 62 | 65 65 6e 20 74 65 73 74 |10 has b|een test|
|00001000| 65 64 20 73 75 63 63 65 | 73 73 66 75 6c 6c 79 20 |ed succe|ssfully |
|00001010| 77 69 74 68 20 53 74 72 | 6f 6e 67 41 52 4d 20 61 |with Str|ongARM a|
|00001020| 6e 64 0a 20 20 20 20 20 | 20 20 20 20 20 20 20 20 |nd. | |
|00001030| 20 52 49 53 43 20 4f 53 | 20 33 2e 37 2c 20 73 6f | RISC OS| 3.7, so|
|00001040| 20 49 20 61 73 73 75 6d | 65 20 74 68 69 73 20 76 | I assum|e this v|
|00001050| 65 72 73 69 6f 6e 20 77 | 69 6c 6c 20 77 6f 72 6b |ersion w|ill work|
|00001060| 2c 20 74 6f 6f 2e 0a 20 | 20 20 20 20 20 20 20 20 |, too.. | |
|00001070| 20 20 20 20 20 52 65 71 | 75 69 72 65 73 20 61 74 | Req|uires at|
|00001080| 20 6c 65 61 73 74 20 32 | 4d 42 20 52 41 4d 20 28 | least 2|MB RAM (|
|00001090| 73 65 65 20 62 65 6c 6f | 77 20 22 53 61 76 69 6e |see belo|w "Savin|
|000010a0| 67 20 6d 65 6d 6f 72 79 | 22 29 2c 20 61 74 0a 20 |g memory|"), at. |
|000010b0| 20 20 20 20 20 20 20 20 | 20 20 20 20 20 6c 65 61 | | lea|
|000010c0| 73 74 20 34 4d 42 20 72 | 65 63 6f 6d 6d 65 6e 64 |st 4MB r|ecommend|
|000010d0| 65 64 2e 0a 53 74 61 74 | 75 73 3a 20 20 20 20 20 |ed..Stat|us: |
|000010e0| 20 20 46 52 45 45 57 41 | 52 45 2c 20 73 65 65 20 | FREEWA|RE, see |
|000010f0| 22 43 6f 70 79 72 69 67 | 68 74 22 20 62 65 6c 6f |"Copyrig|ht" belo|
|00001100| 77 0a 0a 56 65 72 73 69 | 6f 6e 20 31 2e 32 30 20 |w..Versi|on 1.20 |
|00001110| 6f 66 20 74 68 65 20 52 | 49 53 43 20 4f 53 20 70 |of the R|ISC OS p|
|00001120| 6f 72 74 20 6f 66 20 52 | 61 73 4d 6f 6c 20 69 73 |ort of R|asMol is|
|00001130| 20 62 61 73 65 64 20 6f | 6e 20 74 68 65 20 52 61 | based o|n the Ra|
|00001140| 73 4d 6f 6c 20 32 2e 36 | 62 65 74 61 32 0a 73 6f |sMol 2.6|beta2.so|
|00001150| 75 72 63 65 73 2e 20 4e | 6f 74 65 20 74 68 61 74 |urces. N|ote that|
|00001160| 20 74 68 65 20 52 61 73 | 4d 6f 6c 20 68 65 6c 70 | the Ras|Mol help|
|00001170| 20 66 69 6c 65 20 73 74 | 69 6c 6c 20 64 65 73 63 | file st|ill desc|
|00001180| 72 69 62 65 73 20 76 65 | 72 73 69 6f 6e 20 32 2e |ribes ve|rsion 2.|
|00001190| 35 20 6f 66 20 52 61 73 | 4d 6f 6c 2e 0a 55 70 64 |5 of Ras|Mol..Upd|
|000011a0| 61 74 65 64 20 6d 61 6e | 75 61 6c 73 20 69 6e 20 |ated man|uals in |
|000011b0| 68 74 6d 6c 20 66 6f 72 | 6d 61 74 20 61 72 65 20 |html for|mat are |
|000011c0| 61 76 61 69 6c 61 62 6c | 65 20 66 72 6f 6d 20 74 |availabl|e from t|
|000011d0| 68 65 20 57 57 57 20 68 | 6f 6d 65 20 70 61 67 65 |he WWW h|ome page|
|000011e0| 20 28 73 65 65 0a 62 65 | 6c 6f 77 2c 20 22 4c 69 | (see.be|low, "Li|
|000011f0| 6e 6b 73 20 74 6f 20 6d | 6f 6c 65 63 75 6c 65 20 |nks to m|olecule |
|00001200| 64 61 74 61 62 61 6e 6b | 73 20 61 6e 64 20 57 57 |databank|s and WW|
|00001210| 57 20 70 61 67 65 73 20 | 61 62 6f 75 74 20 52 61 |W pages |about Ra|
|00001220| 73 4d 6f 6c 22 29 2e 0a | 0a 46 6f 72 20 69 6e 66 |sMol")..|.For inf|
|00001230| 6f 72 6d 61 74 69 6f 6e | 20 61 62 6f 75 74 20 74 |ormation| about t|
|00001240| 68 65 20 6e 65 77 20 66 | 65 61 74 75 72 65 73 20 |he new f|eatures |
|00001250| 6f 66 20 32 2e 36 62 65 | 74 61 20 32 20 28 6d 6f |of 2.6be|ta 2 (mo|
|00001260| 73 74 20 6e 6f 74 61 62 | 6c 79 20 74 68 65 20 66 |st notab|ly the f|
|00001270| 75 6c 6c 0a 73 75 70 70 | 6f 72 74 20 66 6f 72 20 |ull.supp|ort for |
|00001280| 73 74 65 72 65 6f 20 70 | 69 63 74 75 72 65 73 29 |stereo p|ictures)|
|00001290| 2c 20 72 65 61 64 20 74 | 68 65 20 72 65 6c 65 61 |, read t|he relea|
|000012a0| 73 65 20 6e 6f 74 65 73 | 20 69 6e 20 74 68 65 20 |se notes| in the |
|000012b0| 27 44 6f 63 73 27 20 64 | 69 72 65 63 74 6f 72 79 |'Docs' d|irectory|
|000012c0| 2e 0a 0a 43 6f 6e 74 65 | 6e 74 73 3a 0a 20 20 2a |...Conte|nts:. *|
|000012d0| 20 49 6e 74 72 6f 64 75 | 63 74 69 6f 6e 0a 20 20 | Introdu|ction. |
|000012e0| 2a 20 53 74 61 72 74 69 | 6e 67 20 52 61 73 4d 6f |* Starti|ng RasMo|
|000012f0| 6c 0a 20 20 2a 20 46 69 | 72 73 74 20 53 74 65 70 |l. * Fi|rst Step|
|00001300| 73 0a 20 20 2a 20 4c 6f | 61 64 69 6e 67 20 66 69 |s. * Lo|ading fi|
|00001310| 6c 65 73 0a 20 20 2a 20 | 57 69 6e 64 6f 77 20 73 |les. * |Window s|
|00001320| 69 7a 65 0a 20 20 2a 20 | 54 68 65 20 74 6f 6f 6c |ize. * |The tool|
|00001330| 20 62 61 72 3a 20 53 65 | 6c 65 63 74 69 6f 6e 2c | bar: Se|lection,|
|00001340| 20 52 6f 74 61 74 69 6f | 6e 2c 20 54 72 61 6e 73 | Rotatio|n, Trans|
|00001350| 6c 61 74 69 6f 6e 2c 20 | 5a 6f 6f 6d 69 6e 67 2c |lation, |Zooming,|
|00001360| 20 5a 2d 73 6c 61 62 62 | 69 6e 67 0a 20 20 2a 20 | Z-slabb|ing. * |
|00001370| 44 69 73 70 6c 61 79 20 | 71 75 61 6c 69 74 79 20 |Display |quality |
|00001380| 61 6e 64 20 64 69 74 68 | 65 72 69 6e 67 0a 20 20 |and dith|ering. |
|00001390| 2a 20 53 61 76 69 6e 67 | 20 61 6e 64 20 65 78 70 |* Saving| and exp|
|000013a0| 6f 72 74 69 6e 67 0a 20 | 20 2a 20 43 6f 6e 66 69 |orting. | * Confi|
|000013b0| 67 75 72 61 74 69 6f 6e | 0a 20 20 2a 20 53 61 76 |guration|. * Sav|
|000013c0| 69 6e 67 20 6d 65 6d 6f | 72 79 0a 20 20 2a 20 53 |ing memo|ry. * S|
|000013d0| 63 72 69 70 74 20 66 69 | 6c 65 73 0a 20 20 2a 20 |cript fi|les. * |
|000013e0| 50 43 20 73 63 72 69 70 | 74 20 64 69 72 65 63 74 |PC scrip|t direct|
|000013f0| 6f 72 69 65 73 0a 20 20 | 2a 20 44 69 73 70 6c 61 |ories. |* Displa|
|00001400| 79 20 74 79 70 65 73 0a | 20 20 2a 20 54 68 65 20 |y types.| * The |
|00001410| 56 69 65 77 20 73 75 62 | 2d 6d 65 6e 75 20 61 6e |View sub|-menu an|
|00001420| 64 20 74 68 65 20 22 44 | 6f 74 20 73 75 72 66 61 |d the "D|ot surfa|
|00001430| 63 65 22 20 6f 70 74 69 | 6f 6e 0a 20 20 2a 20 43 |ce" opti|on. * C|
|00001440| 6f 6c 6f 75 72 73 0a 20 | 20 2a 20 54 68 65 20 52 |olours. | * The R|
|00001450| 61 73 4d 6f 6c 20 43 6f | 6d 6d 61 6e 64 20 4c 69 |asMol Co|mmand Li|
|00001460| 6e 65 0a 20 20 2a 20 41 | 64 64 69 74 69 6f 6e 61 |ne. * A|dditiona|
|00001470| 6c 20 66 69 6c 65 20 74 | 79 70 65 73 0a 20 20 2a |l file t|ypes. *|
|00001480| 20 4c 69 6e 6b 73 20 74 | 6f 20 6d 6f 6c 65 63 75 | Links t|o molecu|
|00001490| 6c 65 20 64 61 74 61 62 | 61 6e 6b 73 20 61 6e 64 |le datab|anks and|
|000014a0| 20 57 57 57 20 70 61 67 | 65 73 20 61 62 6f 75 74 | WWW pag|es about|
|000014b0| 20 52 61 73 4d 6f 6c 0a | 20 20 2a 20 48 69 73 74 | RasMol.| * Hist|
|000014c0| 6f 72 79 0a 20 20 2a 20 | 48 6f 77 20 74 6f 20 63 |ory. * |How to c|
|000014d0| 6f 6e 74 61 63 74 20 74 | 68 65 20 61 75 74 68 6f |ontact t|he autho|
|000014e0| 72 73 0a 20 20 2a 20 43 | 6f 70 79 72 69 67 68 74 |rs. * C|opyright|
|000014f0| 0a 20 20 0a 20 20 52 61 | 73 4d 6f 6c 32 20 69 73 |. . Ra|sMol2 is|
|00001500| 20 61 20 6d 6f 6c 65 63 | 75 6c 61 72 20 67 72 61 | a molec|ular gra|
|00001510| 70 68 69 63 73 20 70 72 | 6f 67 72 61 6d 20 69 6e |phics pr|ogram in|
|00001520| 74 65 6e 64 65 64 20 66 | 6f 72 20 74 68 65 20 76 |tended f|or the v|
|00001530| 69 73 75 61 6c 69 73 61 | 74 69 6f 6e 20 6f 66 0a |isualisa|tion of.|
|00001540| 70 72 6f 74 65 69 6e 73 | 2c 20 6e 75 63 6c 65 69 |proteins|, nuclei|
|00001550| 63 20 61 63 69 64 73 20 | 61 6e 64 20 73 6d 61 6c |c acids |and smal|
|00001560| 6c 20 6d 6f 6c 65 63 75 | 6c 65 73 2e 20 54 68 65 |l molecu|les. The|
|00001570| 20 70 72 6f 67 72 61 6d | 20 69 73 20 61 69 6d 65 | program| is aime|
|00001580| 64 20 61 74 20 64 69 73 | 70 6c 61 79 2c 0a 74 65 |d at dis|play,.te|
|00001590| 61 63 68 69 6e 67 20 61 | 6e 64 20 67 65 6e 65 72 |aching a|nd gener|
|000015a0| 61 74 69 6f 6e 20 6f 66 | 20 70 75 62 6c 69 63 61 |ation of| publica|
|000015b0| 74 69 6f 6e 20 71 75 61 | 6c 69 74 79 20 69 6d 61 |tion qua|lity ima|
|000015c0| 67 65 73 2e 20 52 61 73 | 4d 6f 6c 20 72 75 6e 73 |ges. Ras|Mol runs|
|000015d0| 20 6f 6e 0a 4d 69 63 72 | 6f 73 6f 66 74 20 57 69 | on.Micr|osoft Wi|
|000015e0| 6e 64 6f 77 73 2c 20 41 | 70 70 6c 65 20 4d 61 63 |ndows, A|pple Mac|
|000015f0| 69 6e 74 6f 73 68 2c 20 | 41 63 6f 72 6e 20 52 49 |intosh, |Acorn RI|
|00001600| 53 43 20 4f 53 2c 20 55 | 4e 49 58 20 61 6e 64 20 |SC OS, U|NIX and |
|00001610| 56 4d 53 20 73 79 73 74 | 65 6d 73 2e 20 54 68 65 |VMS syst|ems. The|
|00001620| 0a 55 4e 49 58 20 61 6e | 64 20 56 4d 53 20 73 79 |.UNIX an|d VMS sy|
|00001630| 73 74 65 6d 73 20 72 65 | 71 75 69 72 65 20 61 6e |stems re|quire an|
|00001640| 20 38 2c 20 32 34 20 6f | 72 20 33 32 20 62 69 74 | 8, 24 o|r 32 bit|
|00001650| 20 63 6f 6c 6f 75 72 20 | 58 20 57 69 6e 64 6f 77 | colour |X Window|
|00001660| 73 20 64 69 73 70 6c 61 | 79 0a 28 58 31 31 52 34 |s displa|y.(X11R4|
|00001670| 20 6f 72 20 6c 61 74 65 | 72 29 2e 20 54 68 65 20 | or late|r). The |
|00001680| 70 72 6f 67 72 61 6d 20 | 72 65 61 64 73 20 69 6e |program |reads in|
|00001690| 20 61 20 6d 6f 6c 65 63 | 75 6c 65 20 63 6f 2d 6f | a molec|ule co-o|
|000016a0| 72 64 69 6e 61 74 65 20 | 66 69 6c 65 20 61 6e 64 |rdinate |file and|
|000016b0| 0a 69 6e 74 65 72 61 63 | 74 69 76 65 6c 79 20 64 |.interac|tively d|
|000016c0| 69 73 70 6c 61 79 73 20 | 74 68 65 20 6d 6f 6c 65 |isplays |the mole|
|000016d0| 63 75 6c 65 20 6f 6e 20 | 74 68 65 20 73 63 72 65 |cule on |the scre|
|000016e0| 65 6e 20 69 6e 20 61 20 | 76 61 72 69 65 74 79 20 |en in a |variety |
|000016f0| 6f 66 20 63 6f 6c 6f 75 | 72 0a 73 63 68 65 6d 65 |of colou|r.scheme|
|00001700| 73 20 61 6e 64 20 6d 6f | 6c 65 63 75 6c 65 20 72 |s and mo|lecule r|
|00001710| 65 70 72 65 73 65 6e 74 | 61 74 69 6f 6e 73 2e 20 |epresent|ations. |
|00001720| 43 75 72 72 65 6e 74 6c | 79 20 61 76 61 69 6c 61 |Currentl|y availa|
|00001730| 62 6c 65 20 72 65 70 72 | 65 73 65 6e 74 61 74 69 |ble repr|esentati|
|00001740| 6f 6e 73 0a 69 6e 63 6c | 75 64 65 20 64 65 70 74 |ons.incl|ude dept|
|00001750| 68 2d 63 75 65 64 20 77 | 69 72 65 66 72 61 6d 65 |h-cued w|ireframe|
|00001760| 73 2c 20 27 44 72 65 69 | 64 69 6e 67 27 20 73 74 |s, 'Drei|ding' st|
|00001770| 69 63 6b 73 2c 20 73 70 | 61 63 65 66 69 6c 6c 69 |icks, sp|acefilli|
|00001780| 6e 67 20 28 43 50 4b 29 | 20 73 70 68 65 72 65 73 |ng (CPK)| spheres|
|00001790| 2c 0a 62 61 6c 6c 20 61 | 6e 64 20 73 74 69 63 6b |,.ball a|nd stick|
|000017a0| 2c 20 73 6f 6c 69 64 20 | 61 6e 64 20 73 74 72 61 |, solid |and stra|
|000017b0| 6e 64 20 62 69 6f 6d 6f | 6c 65 63 75 6c 61 72 20 |nd biomo|lecular |
|000017c0| 72 69 62 62 6f 6e 73 2c | 20 61 74 6f 6d 20 6c 61 |ribbons,| atom la|
|000017d0| 62 65 6c 73 20 61 6e 64 | 20 64 6f 74 0a 73 75 72 |bels and| dot.sur|
|000017e0| 66 61 63 65 73 2e 0a 0a | 20 20 54 68 65 20 52 61 |faces...| The Ra|
|000017f0| 73 4d 6f 6c 20 68 65 6c | 70 20 66 61 63 69 6c 69 |sMol hel|p facili|
|00001800| 74 79 20 63 61 6e 20 62 | 65 20 61 63 63 65 73 73 |ty can b|e access|
|00001810| 65 64 20 62 79 20 74 79 | 70 69 6e 67 20 22 68 65 |ed by ty|ping "he|
|00001820| 6c 70 20 3c 74 6f 70 69 | 63 3e 22 20 6f 72 20 22 |lp <topi|c>" or "|
|00001830| 68 65 6c 70 0a 3c 74 6f | 70 69 63 3e 20 3c 73 75 |help.<to|pic> <su|
|00001840| 62 74 6f 70 69 63 3e 22 | 20 66 72 6f 6d 20 74 68 |btopic>"| from th|
|00001850| 65 20 52 61 73 4d 6f 6c | 20 63 6f 6d 6d 61 6e 64 |e RasMol| command|
|00001860| 20 6c 69 6e 65 2e 20 41 | 20 63 6f 6d 70 6c 65 74 | line. A| complet|
|00001870| 65 20 6c 69 73 74 20 6f | 66 20 52 61 73 4d 6f 6c |e list o|f RasMol|
|00001880| 0a 63 6f 6d 6d 61 6e 64 | 73 20 6d 61 79 20 62 65 |.command|s may be|
|00001890| 20 64 69 73 70 6c 61 79 | 65 64 20 62 79 20 74 79 | display|ed by ty|
|000018a0| 70 69 6e 67 20 22 68 65 | 6c 70 20 63 6f 6d 6d 61 |ping "he|lp comma|
|000018b0| 6e 64 73 22 2e 20 41 20 | 73 69 6e 67 6c 65 20 71 |nds". A |single q|
|000018c0| 75 65 73 74 69 6f 6e 20 | 6d 61 72 6b 0a 6d 61 79 |uestion |mark.may|
|000018d0| 20 61 6c 73 6f 20 62 65 | 20 75 73 65 64 20 74 6f | also be| used to|
|000018e0| 20 61 62 62 72 65 76 69 | 61 74 65 20 74 68 65 20 | abbrevi|ate the |
|000018f0| 6b 65 79 77 6f 72 64 20 | 22 68 65 6c 70 22 2e 0a |keyword |"help"..|
|00001900| 0a 20 20 43 6f 70 79 72 | 69 67 68 74 20 28 63 29 |. Copyr|ight (c)|
|00001910| 20 31 39 39 32 2d 31 39 | 39 35 20 62 79 20 52 6f | 1992-19|95 by Ro|
|00001920| 67 65 72 20 53 61 79 6c | 65 20 28 72 61 73 33 32 |ger Sayl|e (ras32|
|00001930| 34 32 35 40 67 67 72 2e | 63 6f 2e 75 6b 29 0a 0a |425@ggr.|co.uk)..|
|00001940| 0a 20 53 74 61 72 74 69 | 6e 67 20 52 61 73 4d 6f |. Starti|ng RasMo|
|00001950| 6c 0a 20 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |l. -----|--------|
|00001960| 2d 2d 0a 20 20 57 68 65 | 6e 20 73 74 61 72 74 65 |--. Whe|n starte|
|00001970| 64 20 28 62 79 20 64 6f | 75 62 6c 65 2d 63 6c 69 |d (by do|uble-cli|
|00001980| 63 6b 69 6e 67 20 6f 6e | 20 74 68 65 20 61 70 70 |cking on| the app|
|00001990| 6c 69 63 61 74 69 6f 6e | 20 69 74 73 65 6c 66 20 |lication| itself |
|000019a0| 6f 72 20 6f 6e 20 61 20 | 66 69 6c 65 20 77 68 69 |or on a |file whi|
|000019b0| 63 68 0a 52 61 73 4d 6f | 6c 20 75 6e 64 65 72 73 |ch.RasMo|l unders|
|000019c0| 74 61 6e 64 73 29 2c 20 | 52 61 73 4d 6f 6c 20 69 |tands), |RasMol i|
|000019d0| 6e 73 74 61 6c 6c 73 20 | 69 74 73 65 6c 66 20 6f |nstalls |itself o|
|000019e0| 6e 74 6f 20 74 68 65 20 | 69 63 6f 6e 20 62 61 72 |nto the |icon bar|
|000019f0| 20 61 6e 64 20 6f 70 65 | 6e 73 20 74 77 6f 0a 77 | and ope|ns two.w|
|00001a00| 69 6e 64 6f 77 73 2e 20 | 54 68 65 73 65 20 61 72 |indows. |These ar|
|00001a10| 65 20 74 68 65 20 4d 6f | 6c 65 63 75 6c 65 20 77 |e the Mo|lecule w|
|00001a20| 69 6e 64 6f 77 20 28 62 | 6c 61 63 6b 29 20 61 6e |indow (b|lack) an|
|00001a30| 64 20 74 68 65 20 52 61 | 73 4d 6f 6c 20 43 6f 6d |d the Ra|sMol Com|
|00001a40| 6d 61 6e 64 20 4c 69 6e | 65 0a 77 69 6e 64 6f 77 |mand Lin|e.window|
|00001a50| 2e 20 54 68 65 20 4d 6f | 6c 65 63 75 6c 65 20 77 |. The Mo|lecule w|
|00001a60| 69 6e 64 6f 77 20 64 69 | 73 70 6c 61 79 73 20 74 |indow di|splays t|
|00001a70| 68 65 20 63 75 72 72 65 | 6e 74 6c 79 20 6c 6f 61 |he curre|ntly loa|
|00001a80| 64 65 64 20 6d 6f 6c 65 | 63 75 6c 65 20 61 6e 64 |ded mole|cule and|
|00001a90| 20 61 6c 6c 6f 77 73 0a | 79 6f 75 20 74 6f 20 72 | allows.|you to r|
|00001aa0| 6f 74 61 74 65 2f 74 72 | 61 6e 73 6c 61 74 65 2f |otate/tr|anslate/|
|00001ab0| 7a 2d 73 6c 61 62 20 69 | 74 20 75 73 69 6e 67 20 |z-slab i|t using |
|00001ac0| 74 68 65 20 6d 6f 75 73 | 65 2e 0a 0a 20 46 69 72 |the mous|e... Fir|
|00001ad0| 73 74 20 73 74 65 70 73 | 0a 20 2d 2d 2d 2d 2d 2d |st steps|. ------|
|00001ae0| 2d 2d 2d 2d 2d 0a 20 20 | 54 6f 20 67 65 74 20 61 |-----. |To get a|
|00001af0| 6e 20 69 64 65 61 20 77 | 68 61 74 20 74 68 65 20 |n idea w|hat the |
|00001b00| 70 72 6f 67 72 61 6d 20 | 69 73 20 61 62 6f 75 74 |program |is about|
|00001b10| 2c 20 64 6f 75 62 6c 65 | 2d 63 6c 69 63 6b 20 6f |, double|-click o|
|00001b20| 6e 20 74 68 65 20 66 69 | 6c 65 20 27 31 63 72 6e |n the fi|le '1crn|
|00001b30| 27 20 28 74 68 69 73 0a | 69 73 20 61 20 73 6d 61 |' (this.|is a sma|
|00001b40| 6c 6c 20 70 72 6f 74 65 | 69 6e 20 66 69 6c 65 29 |ll prote|in file)|
|00001b50| 2e 20 49 66 20 79 6f 75 | 20 68 61 76 65 20 6e 6f |. If you| have no|
|00001b60| 74 20 61 6c 72 65 61 64 | 79 20 6c 6f 61 64 65 64 |t alread|y loaded|
|00001b70| 20 52 61 73 4d 6f 6c 2c | 20 69 74 20 73 68 6f 75 | RasMol,| it shou|
|00001b80| 6c 64 20 73 74 61 72 74 | 20 75 70 0a 6e 6f 77 2e |ld start| up.now.|
|00001b90| 20 54 68 65 20 70 72 6f | 74 65 69 6e 20 69 73 20 | The pro|tein is |
|00001ba0| 64 69 73 70 6c 61 79 65 | 64 20 69 6e 20 77 69 72 |displaye|d in wir|
|00001bb0| 65 66 72 61 6d 65 20 6d | 6f 64 65 20 69 6e 20 74 |eframe m|ode in t|
|00001bc0| 68 65 20 4d 6f 6c 65 63 | 75 6c 65 20 77 69 6e 64 |he Molec|ule wind|
|00001bd0| 6f 77 20 28 62 65 68 69 | 6e 64 20 74 68 65 0a 4d |ow (behi|nd the.M|
|00001be0| 6f 6c 65 63 75 6c 65 20 | 77 69 6e 64 6f 77 20 79 |olecule |window y|
|00001bf0| 6f 75 20 63 61 6e 20 61 | 6c 73 6f 20 73 65 65 20 |ou can a|lso see |
|00001c00| 74 68 65 20 43 6f 6d 6d | 61 6e 64 20 4c 69 6e 65 |the Comm|and Line|
|00001c10| 20 77 69 6e 64 6f 77 29 | 2e 20 53 65 6c 65 63 74 | window)|. Select|
|00001c20| 20 74 68 65 20 72 6f 74 | 61 74 69 6f 6e 20 74 6f | the rot|ation to|
|00001c30| 6f 6c 0a 28 74 68 65 20 | 74 6f 6f 6c 20 62 65 6c |ol.(the |tool bel|
|00001c40| 6f 77 20 74 68 65 20 22 | 70 6f 69 6e 74 65 72 22 |ow the "|pointer"|
|00001c50| 20 74 6f 6f 6c 29 2c 20 | 63 6c 69 63 6b 20 53 45 | tool), |click SE|
|00001c60| 4c 45 43 54 20 73 6f 6d | 65 77 68 65 72 65 20 69 |LECT som|ewhere i|
|00001c70| 6e 20 74 68 65 20 4d 6f | 6c 65 63 75 6c 65 20 77 |n the Mo|lecule w|
|00001c80| 69 6e 64 6f 77 0a 61 6e | 64 20 64 72 61 67 20 68 |indow.an|d drag h|
|00001c90| 6f 72 69 7a 6f 6e 74 61 | 6c 6c 79 20 6f 72 20 76 |orizonta|lly or v|
|00001ca0| 65 72 74 69 63 61 6c 6c | 79 2e 20 54 68 69 73 20 |erticall|y. This |
|00001cb0| 72 6f 74 61 74 65 73 20 | 74 68 65 20 6d 6f 6c 65 |rotates |the mole|
|00001cc0| 63 75 6c 65 20 61 62 6f | 75 74 20 74 68 65 20 78 |cule abo|ut the x|
|00001cd0| 2f 79 2d 61 78 65 73 2e | 0a 55 73 69 6e 67 20 41 |/y-axes.|.Using A|
|00001ce0| 44 4a 55 53 54 2c 20 79 | 6f 75 20 63 61 6e 20 72 |DJUST, y|ou can r|
|00001cf0| 6f 74 61 74 65 20 61 62 | 6f 75 74 20 74 68 65 20 |otate ab|out the |
|00001d00| 7a 2d 61 78 69 73 2e 20 | 4e 6f 77 20 63 6c 69 63 |z-axis. |Now clic|
|00001d10| 6b 20 4d 45 4e 55 20 61 | 6e 64 20 63 68 6f 6f 73 |k MENU a|nd choos|
|00001d20| 65 20 22 53 70 61 63 65 | 66 69 6c 6c 22 0a 66 72 |e "Space|fill".fr|
|00001d30| 6f 6d 20 74 68 65 20 22 | 44 69 73 70 6c 61 79 22 |om the "|Display"|
|00001d40| 20 73 75 62 2d 6d 65 6e | 75 2e 20 46 6f 72 20 61 | sub-men|u. For a|
|00001d50| 20 6e 69 63 65 20 73 70 | 65 63 75 6c 61 72 20 68 | nice sp|ecular h|
|00001d60| 69 67 68 6c 69 67 68 74 | 69 6e 67 20 65 66 66 65 |ighlight|ing effe|
|00001d70| 63 74 20 63 68 6f 6f 73 | 65 0a 22 53 70 65 63 75 |ct choos|e."Specu|
|00001d80| 6c 61 72 22 20 66 72 6f | 6d 20 74 68 65 20 22 4f |lar" fro|m the "O|
|00001d90| 70 74 69 6f 6e 73 22 20 | 73 75 62 2d 6d 65 6e 75 |ptions" |sub-menu|
|00001da0| 20 28 64 6f 20 6e 6f 74 | 20 74 72 79 20 22 53 68 | (do not| try "Sh|
|00001db0| 61 64 6f 77 73 22 20 61 | 73 20 69 74 20 69 73 20 |adows" a|s it is |
|00001dc0| 76 65 72 79 20 73 6c 6f | 77 29 2e 0a 49 66 20 79 |very slo|w)..If y|
|00001dd0| 6f 75 20 61 72 65 20 69 | 6e 20 61 20 31 36 20 6f |ou are i|n a 16 o|
|00001de0| 72 20 32 35 36 20 63 6f | 6c 6f 75 72 20 6d 6f 64 |r 256 co|lour mod|
|00001df0| 65 2c 20 74 72 79 20 74 | 68 65 20 74 6f 6f 6c 20 |e, try t|he tool |
|00001e00| 61 74 20 74 68 65 20 62 | 6f 74 74 6f 6d 20 6f 66 |at the b|ottom of|
|00001e10| 20 74 68 65 20 74 6f 6f | 6c 62 61 72 0a 77 68 69 | the too|lbar.whi|
|00001e20| 63 68 20 64 69 74 68 65 | 72 73 20 74 68 65 20 69 |ch dithe|rs the i|
|00001e30| 6d 61 67 65 20 74 6f 20 | 74 68 65 20 63 75 72 72 |mage to |the curr|
|00001e40| 65 6e 74 20 70 61 6c 65 | 74 74 65 2e 20 54 68 69 |ent pale|tte. Thi|
|00001e50| 73 20 69 6d 70 72 6f 76 | 65 73 20 74 68 65 20 64 |s improv|es the d|
|00001e60| 69 73 70 6c 61 79 20 71 | 75 61 6c 69 74 79 0a 73 |isplay q|uality.s|
|00001e70| 69 67 6e 69 66 69 63 61 | 6e 74 6c 79 20 62 75 74 |ignifica|ntly but|
|00001e80| 20 69 74 20 74 61 6b 65 | 73 20 61 20 66 65 77 20 | it take|s a few |
|00001e90| 73 65 63 6f 6e 64 73 2e | 0a 20 20 54 6f 20 74 65 |seconds.|. To te|
|00001ea0| 73 74 20 6f 74 68 65 72 | 20 77 61 79 73 20 6f 66 |st other| ways of|
|00001eb0| 20 64 69 73 70 6c 61 79 | 69 6e 67 20 74 68 65 20 | display|ing the |
|00001ec0| 6d 6f 6c 65 63 75 6c 65 | 2c 20 74 72 79 20 61 6c |molecule|, try al|
|00001ed0| 73 6f 20 22 42 61 6c 6c | 26 53 74 69 63 6b 22 20 |so "Ball|&Stick" |
|00001ee0| 61 6e 64 20 22 42 61 63 | 6b 2d 0a 62 6f 6e 65 22 |and "Bac|k-.bone"|
|00001ef0| 20 66 72 6f 6d 20 74 68 | 65 20 22 44 69 73 70 6c | from th|e "Displ|
|00001f00| 61 79 22 20 73 75 62 2d | 6d 65 6e 75 2e 20 57 68 |ay" sub-|menu. Wh|
|00001f10| 69 6c 65 20 62 65 69 6e | 67 20 69 6e 20 22 42 61 |ile bein|g in "Ba|
|00001f20| 63 6b 62 6f 6e 65 22 20 | 6d 6f 64 65 2c 20 73 65 |ckbone" |mode, se|
|00001f30| 6c 65 63 74 20 74 68 65 | 0a 74 72 61 6e 73 6c 61 |lect the|.transla|
|00001f40| 74 69 6f 6e 20 74 6f 6f | 6c 20 28 74 68 65 20 6f |tion too|l (the o|
|00001f50| 6e 65 20 62 65 6c 6f 77 | 20 74 68 65 20 72 6f 74 |ne below| the rot|
|00001f60| 61 74 69 6f 6e 20 74 6f | 6f 6c 29 2e 20 43 6c 69 |ation to|ol). Cli|
|00001f70| 63 6b 20 41 44 4a 55 53 | 54 20 73 6f 6d 65 77 68 |ck ADJUS|T somewh|
|00001f80| 65 72 65 20 69 6e 20 74 | 68 65 0a 77 69 6e 64 6f |ere in t|he.windo|
|00001f90| 77 20 61 6e 64 20 64 72 | 61 67 20 73 6c 6f 77 6c |w and dr|ag slowl|
|00001fa0| 79 20 28 21 29 20 76 65 | 72 74 69 63 61 6c 6c 79 |y (!) ve|rtically|
|00001fb0| 20 74 6f 20 7a 6f 6f 6d | 20 69 6e 2f 6f 75 74 2e | to zoom| in/out.|
|00001fc0| 0a 0a 4e 6f 74 65 20 74 | 68 61 74 20 74 68 65 20 |..Note t|hat the |
|00001fd0| 70 72 6f 67 72 61 6d 20 | 69 73 20 66 75 6c 6c 79 |program |is fully|
|00001fe0| 20 6d 75 6c 74 69 74 61 | 73 6b 69 6e 67 2c 20 65 | multita|sking, e|
|00001ff0| 76 65 6e 20 77 68 69 6c | 65 20 63 61 6c 63 75 6c |ven whil|e calcul|
|00002000| 61 74 69 6e 67 20 63 6f | 6d 70 6c 65 78 20 69 6d |ating co|mplex im|
|00002010| 61 67 65 73 0a 6c 69 6b | 65 20 64 6f 74 20 73 75 |ages.lik|e dot su|
|00002020| 72 66 61 63 65 73 20 6f | 72 20 73 68 61 64 6f 77 |rfaces o|r shadow|
|00002030| 73 2e 20 57 68 69 6c 65 | 20 74 68 65 20 70 72 6f |s. While| the pro|
|00002040| 67 72 61 6d 20 69 73 20 | 63 61 6c 63 75 6c 61 74 |gram is |calculat|
|00002050| 69 6e 67 20 74 68 65 20 | 70 6f 69 6e 74 65 72 20 |ing the |pointer |
|00002060| 63 68 61 6e 67 65 73 0a | 74 6f 20 61 6e 20 68 6f |changes.|to an ho|
|00002070| 75 72 67 6c 61 73 73 20 | 77 68 69 6c 65 20 69 74 |urglass |while it|
|00002080| 20 69 73 20 69 6e 73 69 | 64 65 20 74 68 65 20 52 | is insi|de the R|
|00002090| 61 73 4d 6f 6c 20 77 69 | 6e 64 6f 77 2e 0a 0a 20 |asMol wi|ndow... |
|000020a0| 4c 6f 61 64 69 6e 67 20 | 66 69 6c 65 73 0a 20 2d |Loading |files. -|
|000020b0| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 0a 20 20 41 |--------|----. A|
|000020c0| 20 4d 6f 6c 65 63 75 6c | 65 20 66 69 6c 65 73 20 | Molecul|e files |
|000020d0| 6d 61 79 20 62 65 20 6c | 6f 61 64 65 64 20 62 79 |may be l|oaded by|
|000020e0| 20 64 6f 75 62 6c 65 2d | 63 6c 69 63 6b 69 6e 67 | double-|clicking|
|000020f0| 20 6f 6e 20 69 74 20 6f | 72 20 62 79 20 64 72 61 | on it o|r by dra|
|00002100| 67 67 69 6e 67 20 69 74 | 0a 74 6f 20 74 68 65 20 |gging it|.to the |
|00002110| 52 61 73 4d 6f 6c 20 69 | 63 6f 6e 20 6f 6e 20 74 |RasMol i|con on t|
|00002120| 68 65 20 69 63 6f 6e 20 | 62 61 72 20 6f 72 20 74 |he icon |bar or t|
|00002130| 6f 20 74 68 65 20 4d 6f | 6c 65 63 75 6c 65 20 77 |o the Mo|lecule w|
|00002140| 69 6e 64 6f 77 2e 0a 20 | 20 44 72 61 67 67 69 6e |indow.. | Draggin|
|00002150| 67 20 61 20 66 69 6c 65 | 20 74 6f 20 74 68 65 20 |g a file| to the |
|00002160| 43 6f 6d 6d 61 6e 64 20 | 4c 69 6e 65 20 77 69 6e |Command |Line win|
|00002170| 64 6f 77 20 63 61 75 73 | 65 73 20 69 74 73 20 66 |dow caus|es its f|
|00002180| 75 6c 6c 20 70 61 74 68 | 20 6e 61 6d 65 20 74 6f |ull path| name to|
|00002190| 20 62 65 0a 69 6e 73 65 | 72 74 65 64 20 61 74 20 | be.inse|rted at |
|000021a0| 74 68 65 20 63 61 72 65 | 74 20 70 6f 73 69 74 69 |the care|t positi|
|000021b0| 6f 6e 2e 20 54 68 69 73 | 20 6d 61 6b 65 73 20 6c |on. This| makes l|
|000021c0| 6f 61 64 69 6e 67 20 66 | 69 6c 65 73 20 66 72 6f |oading f|iles fro|
|000021d0| 6d 20 74 68 65 20 63 6f | 6d 6d 61 6e 64 20 6c 69 |m the co|mmand li|
|000021e0| 6e 65 0a 65 61 73 69 65 | 72 2e 0a 0a 20 43 75 72 |ne.easie|r... Cur|
|000021f0| 72 65 6e 74 6c 79 20 72 | 65 63 6f 67 6e 69 73 65 |rently r|ecognise|
|00002200| 64 20 66 69 6c 65 74 79 | 70 65 73 20 28 61 6c 6c |d filety|pes (all|
|00002210| 6f 63 61 74 65 64 20 62 | 79 20 41 63 6f 72 6e 29 |ocated b|y Acorn)|
|00002220| 20 61 72 65 3a 0a 0a 20 | 49 6e 64 75 73 74 72 79 | are:.. |Industry|
|00002230| 20 73 74 61 6e 64 61 72 | 64 20 6e 61 6d 65 20 20 | standar|d name |
|00002240| 20 20 20 20 20 20 20 20 | 20 20 20 20 44 4f 53 20 | | DOS |
|00002250| 65 78 74 2e 20 20 20 52 | 49 53 43 20 4f 53 20 6e |ext. R|ISC OS n|
|00002260| 61 6d 65 20 20 74 79 70 | 65 0a 20 2d 2d 2d 2d 2d |ame typ|e. -----|
|00002270| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00002280| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00002290| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|000022a0| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 0a 20 42 72 |--------|----. Br|
|000022b0| 6f 6f 6b 68 61 76 65 6e | 20 50 72 6f 74 65 69 6e |ookhaven| Protein|
|000022c0| 20 44 61 74 61 20 42 61 | 6e 6b 20 66 69 6c 65 73 | Data Ba|nk files|
|000022d0| 20 20 50 44 42 20 20 20 | 20 20 20 20 20 50 44 42 | PDB | PDB|
|000022e0| 20 20 20 20 20 20 20 20 | 20 20 20 31 32 41 0a 20 | | 12A. |
|000022f0| 41 6c 63 68 65 6d 79 20 | 66 69 6c 65 73 20 20 20 |Alchemy |files |
|00002300| 20 20 20 20 20 20 20 20 | 20 20 20 20 20 20 20 20 | | |
|00002310| 20 20 20 20 41 4c 43 20 | 20 20 20 20 20 20 20 41 | ALC | A|
|00002320| 6c 63 68 65 6d 79 20 20 | 20 20 20 20 20 31 32 39 |lchemy | 129|
|00002330| 0a 20 4d 6f 6c 65 63 75 | 6c 61 72 20 44 65 73 69 |. Molecu|lar Desi|
|00002340| 67 6e 20 4c 74 64 2e 20 | 4d 4f 4c 20 66 69 6c 65 |gn Ltd. |MOL file|
|00002350| 73 20 20 20 20 20 4d 4f | 4c 20 20 20 20 20 20 20 |s MO|L |
|00002360| 20 4d 4f 4c 20 20 20 20 | 20 20 20 20 20 20 20 31 | MOL | 1|
|00002370| 32 38 0a 20 4d 4f 50 41 | 43 20 66 69 6c 65 73 20 |28. MOPA|C files |
|00002380| 20 20 20 20 20 20 20 20 | 20 20 20 20 20 20 20 20 | | |
|00002390| 20 20 20 20 20 20 20 20 | 3f 3f 3f 20 20 20 20 20 | |??? |
|000023a0| 20 20 20 4d 4f 50 41 43 | 20 20 20 20 20 20 20 20 | MOPAC| |
|000023b0| 20 31 32 37 0a 20 52 61 | 73 4d 6f 6c 20 73 63 72 | 127. Ra|sMol scr|
|000023c0| 69 70 74 20 66 69 6c 65 | 73 20 20 20 20 20 20 20 |ipt file|s |
|000023d0| 20 20 20 20 20 20 20 20 | 20 20 53 43 52 20 20 20 | | SCR |
|000023e0| 20 20 20 20 20 52 61 73 | 4d 6f 6c 53 63 20 20 20 | Ras|MolSc |
|000023f0| 20 20 20 31 32 42 0a 0a | 4e 6f 74 65 20 74 68 61 | 12B..|Note tha|
|00002400| 74 20 66 69 6c 65 73 20 | 68 61 76 65 20 74 6f 20 |t files |have to |
|00002410| 62 65 20 66 69 6c 65 74 | 79 70 65 64 20 63 6f 72 |be filet|yped cor|
|00002420| 72 65 63 74 6c 79 20 69 | 6e 20 6f 72 64 65 72 20 |rectly i|n order |
|00002430| 74 6f 20 62 65 20 6c 6f | 61 64 65 64 20 62 79 0a |to be lo|aded by.|
|00002440| 52 61 73 4d 6f 6c 2e 20 | 49 66 20 79 6f 75 20 6c |RasMol. |If you l|
|00002450| 6f 61 64 20 61 20 66 69 | 6c 65 20 61 6e 64 20 61 |oad a fi|le and a|
|00002460| 6c 6c 20 79 6f 75 20 73 | 65 65 20 69 73 20 61 20 |ll you s|ee is a |
|00002470| 62 6c 61 63 6b 20 77 69 | 6e 64 6f 77 20 74 68 65 |black wi|ndow the|
|00002480| 6e 20 6d 6f 73 74 0a 70 | 72 6f 62 61 62 6c 79 20 |n most.p|robably |
|00002490| 74 68 65 20 66 69 6c 65 | 20 64 6f 65 73 20 6e 6f |the file| does no|
|000024a0| 74 20 63 6f 6e 74 61 69 | 6e 20 61 6e 79 20 63 6f |t contai|n any co|
|000024b0| 6e 6e 65 63 74 69 76 69 | 74 79 20 69 6e 66 6f 72 |nnectivi|ty infor|
|000024c0| 6d 61 74 69 6f 6e 2e 20 | 54 72 79 0a 65 6e 74 65 |mation. |Try.ente|
|000024d0| 72 69 6e 67 20 22 63 6f | 6e 6e 65 63 74 22 20 69 |ring "co|nnect" i|
|000024e0| 6e 20 74 68 65 20 63 6f | 6d 6d 61 6e 64 20 6c 69 |n the co|mmand li|
|000024f0| 6e 65 20 77 69 6e 64 6f | 77 2e 0a 0a 20 57 69 6e |ne windo|w... Win|
|00002500| 64 6f 77 20 73 69 7a 65 | 0a 20 2d 2d 2d 2d 2d 2d |dow size|. ------|
|00002510| 2d 2d 2d 2d 2d 0a 20 20 | 54 68 65 20 73 69 7a 65 |-----. |The size|
|00002520| 20 6f 66 20 74 68 65 20 | 4d 6f 6c 65 63 75 6c 65 | of the |Molecule|
|00002530| 20 77 69 6e 64 6f 77 20 | 64 65 74 65 72 6d 69 6e | window |determin|
|00002540| 65 73 20 74 68 65 20 73 | 70 65 65 64 20 6f 66 20 |es the s|peed of |
|00002550| 74 68 65 20 61 70 70 6c | 69 63 61 74 69 6f 6e 20 |the appl|ication |
|00002560| 61 6e 64 0a 61 6c 73 6f | 20 68 6f 77 20 6d 75 63 |and.also| how muc|
|00002570| 68 20 6d 65 6d 6f 72 79 | 20 69 73 20 75 73 65 64 |h memory| is used|
|00002580| 2e 20 54 68 65 20 64 65 | 66 61 75 6c 74 20 73 69 |. The de|fault si|
|00002590| 7a 65 20 6f 66 20 74 68 | 65 20 64 69 73 70 6c 61 |ze of th|e displa|
|000025a0| 79 20 69 73 20 34 38 30 | 20 62 79 20 34 38 30 0a |y is 480| by 480.|
|000025b0| 70 69 78 65 6c 73 2e 20 | 42 79 20 63 68 6f 6f 73 |pixels. |By choos|
|000025c0| 69 6e 67 20 22 53 63 61 | 6c 65 22 20 66 72 6f 6d |ing "Sca|le" from|
|000025d0| 20 74 68 65 20 6d 61 69 | 6e 20 6d 65 6e 75 20 79 | the mai|n menu y|
|000025e0| 6f 75 20 63 61 6e 20 63 | 68 61 6e 67 65 20 74 68 |ou can c|hange th|
|000025f0| 65 20 73 63 61 6c 69 6e | 67 20 6f 66 0a 74 68 65 |e scalin|g of.the|
|00002600| 20 77 69 6e 64 6f 77 2e | 20 31 30 30 25 20 63 6f | window.| 100% co|
|00002610| 72 72 65 73 70 6f 6e 64 | 73 20 74 6f 20 34 38 30 |rrespond|s to 480|
|00002620| 20 70 69 78 65 6c 2e 20 | 54 68 65 20 77 69 64 74 | pixel. |The widt|
|00002630| 68 20 6f 66 20 74 68 65 | 20 77 69 6e 64 6f 77 20 |h of the| window |
|00002640| 69 73 20 61 0a 70 65 72 | 63 65 6e 74 61 67 65 20 |is a.per|centage |
|00002650| 6f 66 20 69 74 73 20 68 | 65 69 67 68 74 2c 20 73 |of its h|eight, s|
|00002660| 6f 20 61 20 77 69 6e 64 | 6f 77 20 61 74 20 61 20 |o a wind|ow at a |
|00002670| 73 63 61 6c 69 6e 67 20 | 6f 66 20 35 30 25 20 61 |scaling |of 50% a|
|00002680| 6e 64 20 61 20 77 69 64 | 74 68 20 6f 66 20 31 35 |nd a wid|th of 15|
|00002690| 30 25 0a 77 6f 75 6c 64 | 20 62 65 20 32 34 30 20 |0%.would| be 240 |
|000026a0| 70 69 78 65 6c 73 20 68 | 69 67 68 20 61 6e 64 20 |pixels h|igh and |
|000026b0| 33 36 30 20 70 69 78 65 | 6c 73 20 77 69 64 65 2e |360 pixe|ls wide.|
|000026c0| 0a 20 20 54 6f 20 73 65 | 74 20 74 68 65 20 64 65 |. To se|t the de|
|000026d0| 66 61 75 6c 74 20 73 69 | 7a 65 2c 20 63 68 61 6e |fault si|ze, chan|
|000026e0| 67 65 20 74 68 65 20 63 | 6f 6e 66 69 67 75 72 61 |ge the c|onfigura|
|000026f0| 74 69 6f 6e 20 6f 66 20 | 74 68 65 20 70 72 6f 67 |tion of |the prog|
|00002700| 72 61 6d 20 28 73 65 65 | 20 62 65 6c 6f 77 0a 22 |ram (see| below."|
|00002710| 43 6f 6e 66 69 67 75 72 | 61 74 69 6f 6e 22 29 2e |Configur|ation").|
|00002720| 0a 20 20 4e 6f 74 65 20 | 74 68 61 74 20 74 68 65 |. Note |that the|
|00002730| 20 6d 65 6d 6f 72 79 20 | 79 6f 75 20 73 61 76 65 | memory |you save|
|00002740| 20 62 79 20 64 65 63 72 | 65 61 73 69 6e 67 20 74 | by decr|easing t|
|00002750| 68 65 20 77 69 6e 64 6f | 77 20 73 69 7a 65 20 69 |he windo|w size i|
|00002760| 73 20 6e 6f 74 20 67 69 | 76 65 6e 0a 62 61 63 6b |s not gi|ven.back|
|00002770| 20 74 6f 20 74 68 65 20 | 73 79 73 74 65 6d 2c 20 | to the |system, |
|00002780| 73 6f 20 74 6f 20 73 61 | 76 65 20 6d 65 6d 6f 72 |so to sa|ve memor|
|00002790| 79 2c 20 63 68 61 6e 67 | 65 20 74 68 65 20 77 69 |y, chang|e the wi|
|000027a0| 6e 64 6f 77 20 73 69 7a | 65 20 75 73 65 64 20 61 |ndow siz|e used a|
|000027b0| 74 20 73 74 61 72 74 2d | 0a 75 70 20 62 79 20 63 |t start-|.up by c|
|000027c0| 68 61 6e 67 69 6e 67 20 | 74 68 65 20 63 6f 6e 66 |hanging |the conf|
|000027d0| 69 67 75 72 61 74 69 6f | 6e 2e 0a 0a 20 54 68 65 |iguratio|n... The|
|000027e0| 20 74 6f 6f 6c 20 62 61 | 72 3a 20 53 65 6c 65 63 | tool ba|r: Selec|
|000027f0| 74 69 6f 6e 2c 20 52 6f | 74 61 74 69 6f 6e 2c 20 |tion, Ro|tation, |
|00002800| 54 72 61 6e 73 6c 61 74 | 69 6f 6e 2c 20 5a 6f 6f |Translat|ion, Zoo|
|00002810| 6d 69 6e 67 2c 20 5a 2d | 73 6c 61 62 62 69 6e 67 |ming, Z-|slabbing|
|00002820| 0a 20 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |. ------|--------|
|00002830| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00002840| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00002850| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00002860| 2d 2d 2d 2d 2d 0a 20 20 | 54 68 65 20 74 6f 6f 6c |-----. |The tool|
|00002870| 20 62 61 72 20 63 6f 6e | 74 61 69 6e 73 20 66 69 | bar con|tains fi|
|00002880| 76 65 20 74 6f 6f 6c 73 | 2e 20 46 72 6f 6d 20 74 |ve tools|. From t|
|00002890| 6f 70 20 74 6f 20 62 6f | 74 74 6f 6d 20 74 68 65 |op to bo|ttom the|
|000028a0| 73 65 20 61 72 65 3a 0a | 54 68 65 20 73 65 6c 65 |se are:.|The sele|
|000028b0| 63 74 69 6f 6e 20 74 6f | 6f 6c 2c 20 74 68 65 20 |ction to|ol, the |
|000028c0| 72 6f 74 61 74 69 6f 6e | 20 74 6f 6f 6c 2c 20 74 |rotation| tool, t|
|000028d0| 68 65 20 74 72 61 6e 73 | 6c 61 74 69 6f 6e 2f 7a |he trans|lation/z|
|000028e0| 6f 6f 6d 69 6e 67 20 74 | 6f 6f 6c 2c 20 74 68 65 |ooming t|ool, the|
|000028f0| 0a 7a 2d 73 6c 61 62 62 | 69 6e 67 20 74 6f 6f 6c |.z-slabb|ing tool|
|00002900| 20 61 6e 64 20 74 68 65 | 20 64 69 74 68 65 72 69 | and the| ditheri|
|00002910| 6e 67 20 74 6f 6f 6c 2e | 20 54 68 65 20 6c 61 74 |ng tool.| The lat|
|00002920| 74 65 72 20 69 73 20 64 | 65 73 63 72 69 62 65 64 |ter is d|escribed|
|00002930| 20 69 6e 20 64 65 74 61 | 69 6c 0a 69 6e 20 74 68 | in deta|il.in th|
|00002940| 65 20 73 65 63 74 69 6f | 6e 20 22 44 69 73 70 6c |e sectio|n "Displ|
|00002950| 61 79 20 71 75 61 6c 69 | 74 79 20 61 6e 64 20 64 |ay quali|ty and d|
|00002960| 69 74 68 65 72 69 6e 67 | 22 2e 0a 20 20 54 68 65 |ithering|".. The|
|00002970| 20 66 69 72 73 74 20 66 | 6f 75 72 20 64 65 74 65 | first f|our dete|
|00002980| 72 6d 69 6e 65 20 77 68 | 69 63 68 20 69 6e 74 65 |rmine wh|ich inte|
|00002990| 72 61 63 74 69 76 65 20 | 6d 6f 64 65 20 74 68 65 |ractive |mode the|
|000029a0| 20 70 72 6f 67 72 61 6d | 20 69 73 20 69 6e 2c 20 | program| is in, |
|000029b0| 69 2e 65 2e 0a 68 6f 77 | 20 6d 6f 75 73 65 20 63 |i.e..how| mouse c|
|000029c0| 6c 69 63 6b 73 2f 64 72 | 61 67 73 20 61 72 65 20 |licks/dr|ags are |
|000029d0| 69 6e 74 65 72 70 72 65 | 74 65 64 3a 0a 0a 53 65 |interpre|ted:..Se|
|000029e0| 6c 65 63 74 20 6d 6f 64 | 65 3a 20 49 66 20 79 6f |lect mod|e: If yo|
|000029f0| 75 20 63 6c 69 63 6b 20 | 6f 6e 20 61 6e 20 61 74 |u click |on an at|
|00002a00| 6f 6d 2c 20 69 6e 66 6f | 72 6d 61 74 69 6f 6e 20 |om, info|rmation |
|00002a10| 61 62 6f 75 74 20 69 74 | 20 69 73 20 64 69 73 70 |about it| is disp|
|00002a20| 6c 61 79 65 64 20 69 6e | 0a 20 20 20 20 20 20 20 |layed in|. |
|00002a30| 20 20 20 20 20 20 74 68 | 65 20 43 6f 6d 6d 61 6e | th|e Comman|
|00002a40| 64 20 4c 69 6e 65 20 77 | 69 6e 64 6f 77 2e 20 4e |d Line w|indow. N|
|00002a50| 6f 74 65 20 74 68 61 74 | 20 65 76 65 6e 20 74 68 |ote that| even th|
|00002a60| 6f 75 67 68 20 74 68 69 | 73 20 69 73 20 63 61 6c |ough thi|s is cal|
|00002a70| 6c 65 64 0a 20 20 20 20 | 20 20 20 20 20 20 20 20 |led. | |
|00002a80| 20 22 73 65 6c 65 63 74 | 69 6f 6e 20 6d 6f 64 65 | "select|ion mode|
|00002a90| 22 2c 20 69 74 20 68 61 | 73 20 6e 6f 74 68 69 6e |", it ha|s nothin|
|00002aa0| 67 20 74 6f 20 64 6f 20 | 77 69 74 68 20 73 65 6c |g to do |with sel|
|00002ab0| 65 63 74 69 6e 67 20 67 | 72 6f 75 70 73 0a 20 20 |ecting g|roups. |
|00002ac0| 20 20 20 20 20 20 20 20 | 20 20 20 6f 66 20 61 74 | | of at|
|00002ad0| 6f 6d 73 20 6f 72 20 73 | 69 6e 67 6c 65 20 61 74 |oms or s|ingle at|
|00002ae0| 6f 6d 73 20 75 73 69 6e | 67 20 74 68 65 20 63 6f |oms usin|g the co|
|00002af0| 6d 6d 61 6e 64 20 22 73 | 65 6c 65 63 74 22 20 6f |mmand "s|elect" o|
|00002b00| 6e 20 74 68 65 20 63 6f | 6d 6d 61 6e 64 0a 20 20 |n the co|mmand. |
|00002b10| 20 20 20 20 20 20 20 20 | 20 20 20 6c 69 6e 65 20 | | line |
|00002b20| 28 66 6f 72 20 6d 6f 72 | 65 20 69 6e 66 6f 72 6d |(for mor|e inform|
|00002b30| 61 74 69 6f 6e 20 6f 6e | 20 74 68 69 73 20 70 6f |ation on| this po|
|00002b40| 77 65 72 66 75 6c 20 66 | 65 61 74 75 72 65 2c 20 |werful f|eature, |
|00002b50| 74 79 70 65 20 22 68 65 | 6c 70 0a 20 20 20 20 20 |type "he|lp. |
|00002b60| 20 20 20 20 20 20 20 20 | 73 65 6c 65 63 74 22 20 | |select" |
|00002b70| 6f 6e 20 74 68 65 20 63 | 6f 6d 6d 61 6e 64 20 6c |on the c|ommand l|
|00002b80| 69 6e 65 29 2e 0a 20 20 | 20 20 20 20 20 20 20 20 |ine).. | |
|00002b90| 20 20 20 20 20 55 73 69 | 6e 67 20 74 68 65 20 63 | Usi|ng the c|
|00002ba0| 6f 6d 6d 61 6e 64 20 6c | 69 6e 65 20 79 6f 75 20 |ommand l|ine you |
|00002bb0| 63 61 6e 20 61 6c 73 6f | 20 6d 6f 64 69 66 79 20 |can also| modify |
|00002bc0| 74 68 65 20 62 65 68 61 | 76 69 6f 75 72 20 6f 66 |the beha|viour of|
|00002bd0| 0a 20 20 20 20 20 20 20 | 20 20 20 20 20 20 74 68 |. | th|
|00002be0| 65 20 73 65 6c 65 63 74 | 20 6d 6f 64 65 2c 20 65 |e select| mode, e|
|00002bf0| 2e 67 2e 20 79 6f 75 20 | 63 61 6e 20 6d 61 6b 65 |.g. you |can make|
|00002c00| 20 52 61 73 4d 6f 6c 20 | 61 64 64 20 6c 61 62 65 | RasMol |add labe|
|00002c10| 6c 73 20 66 6f 72 20 74 | 68 65 0a 20 20 20 20 20 |ls for t|he. |
|00002c20| 20 20 20 20 20 20 20 20 | 61 74 6f 6d 73 20 79 6f | |atoms yo|
|00002c30| 75 20 63 6c 69 63 6b 20 | 6f 6e 20 62 79 20 74 79 |u click |on by ty|
|00002c40| 70 69 6e 67 20 22 53 65 | 74 20 70 69 63 6b 69 6e |ping "Se|t pickin|
|00002c50| 67 20 6c 61 62 65 6c 22 | 2e 20 53 65 65 20 74 68 |g label"|. See th|
|00002c60| 65 0a 20 20 20 20 20 20 | 20 20 20 20 20 20 20 32 |e. | 2|
|00002c70| 2e 36 62 65 74 61 31 20 | 72 65 6c 65 61 73 65 20 |.6beta1 |release |
|00002c80| 6e 6f 74 65 73 20 66 6f | 72 20 66 75 72 74 68 65 |notes fo|r furthe|
|00002c90| 72 20 6f 70 74 69 6f 6e | 73 2c 20 65 2e 67 2e 20 |r option|s, e.g. |
|00002ca0| 66 6f 72 20 64 69 73 70 | 6c 61 79 69 6e 67 0a 20 |for disp|laying. |
|00002cb0| 20 20 20 20 20 20 20 20 | 20 20 20 20 64 69 73 74 | | dist|
|00002cc0| 61 6e 63 65 73 20 61 6e | 64 20 61 6e 67 6c 65 73 |ances an|d angles|
|00002cd0| 20 62 79 20 63 6c 69 63 | 6b 69 6e 67 20 6f 6e 20 | by clic|king on |
|00002ce0| 61 74 6f 6d 73 2e 0a 52 | 6f 74 61 74 69 6f 6e 20 |atoms..R|otation |
|00002cf0| 6d 6f 64 65 3a 20 44 72 | 61 67 67 69 6e 67 20 68 |mode: Dr|agging h|
|00002d00| 6f 72 69 7a 6f 6e 74 61 | 6c 6c 79 20 75 73 69 6e |orizonta|lly usin|
|00002d10| 67 20 53 45 4c 45 43 54 | 20 72 6f 74 61 74 65 73 |g SELECT| rotates|
|00002d20| 20 74 68 65 20 6d 6f 6c | 65 63 75 6c 65 20 61 62 | the mol|ecule ab|
|00002d30| 6f 75 74 0a 20 20 20 20 | 20 20 20 20 20 20 20 20 |out. | |
|00002d40| 20 20 20 74 68 65 20 79 | 2d 61 78 69 73 2e 20 44 | the y|-axis. D|
|00002d50| 72 61 67 67 69 6e 67 20 | 76 65 72 74 69 63 61 6c |ragging |vertical|
|00002d60| 6c 79 20 75 73 69 6e 67 | 20 53 45 4c 45 43 54 20 |ly using| SELECT |
|00002d70| 72 6f 74 61 74 65 73 20 | 74 68 65 20 6d 6f 6c 65 |rotates |the mole|
|00002d80| 63 75 6c 65 0a 20 20 20 | 20 20 20 20 20 20 20 20 |cule. | |
|00002d90| 20 20 20 20 61 62 6f 75 | 74 20 74 68 65 20 78 2d | abou|t the x-|
|00002da0| 61 78 69 73 2e 20 44 72 | 61 67 67 69 6e 67 20 76 |axis. Dr|agging v|
|00002db0| 65 72 74 69 63 61 6c 6c | 79 20 6f 72 20 68 6f 72 |erticall|y or hor|
|00002dc0| 69 7a 6f 6e 74 61 6c 6c | 79 20 75 73 69 6e 67 20 |izontall|y using |
|00002dd0| 41 44 4a 55 53 54 0a 20 | 20 20 20 20 20 20 20 20 |ADJUST. | |
|00002de0| 20 20 20 20 20 20 72 6f | 74 61 74 65 73 20 74 68 | ro|tates th|
|00002df0| 65 20 6d 6f 6c 65 63 75 | 6c 65 20 61 62 6f 75 74 |e molecu|le about|
|00002e00| 20 74 68 65 20 7a 2d 61 | 78 69 73 2e 0a 20 20 20 | the z-a|xis.. |
|00002e10| 20 20 20 20 20 20 20 20 | 20 20 20 20 4e 6f 74 65 | | Note|
|00002e20| 20 74 68 61 74 20 72 6f | 74 61 74 69 6f 6e 20 77 | that ro|tation w|
|00002e30| 6f 72 6b 73 20 64 69 66 | 66 65 72 65 6e 74 6c 79 |orks dif|ferently|
|00002e40| 20 66 72 6f 6d 20 74 68 | 65 20 77 61 79 20 69 74 | from th|e way it|
|00002e50| 20 77 6f 72 6b 73 20 69 | 6e 0a 20 20 20 20 20 20 | works i|n. |
|00002e60| 20 20 20 20 20 20 20 20 | 20 41 72 74 57 6f 72 6b | | ArtWork|
|00002e70| 73 20 6f 72 20 44 72 61 | 77 20 77 68 65 72 65 20 |s or Dra|w where |
|00002e80| 79 6f 75 20 64 72 61 67 | 20 61 6c 6f 6e 67 20 61 |you drag| along a|
|00002e90| 6e 20 61 72 63 2e 20 49 | 6e 20 52 61 73 4d 6f 6c |n arc. I|n RasMol|
|00002ea0| 20 79 6f 75 0a 20 20 20 | 20 20 20 20 20 20 20 20 | you. | |
|00002eb0| 20 20 20 20 73 68 6f 75 | 6c 64 20 73 69 6d 70 6c | shou|ld simpl|
|00002ec0| 79 20 64 72 61 67 20 65 | 69 74 68 65 72 20 68 6f |y drag e|ither ho|
|00002ed0| 72 69 7a 6f 6e 74 61 6c | 6c 79 20 6f 72 20 76 65 |rizontal|ly or ve|
|00002ee0| 72 74 69 63 61 6c 6c 79 | 2e 0a 54 72 61 6e 73 6c |rtically|..Transl|
|00002ef0| 61 74 69 6f 6e 2f 7a 6f | 6f 6d 20 6d 6f 64 65 3a |ation/zo|om mode:|
|00002f00| 20 44 72 61 67 67 69 6e | 67 20 75 73 69 6e 67 20 | Draggin|g using |
|00002f10| 53 45 4c 45 43 54 20 74 | 72 61 6e 73 6c 61 74 65 |SELECT t|ranslate|
|00002f20| 73 20 28 22 6d 6f 76 65 | 73 22 29 20 74 68 65 20 |s ("move|s") the |
|00002f30| 6d 6f 6c 65 63 75 6c 65 | 0a 20 20 20 20 20 20 20 |molecule|. |
|00002f40| 20 20 20 20 20 20 20 20 | 20 20 20 20 20 20 20 20 | | |
|00002f50| 61 63 63 6f 72 64 69 6e | 67 6c 79 20 69 6e 20 74 |accordin|gly in t|
|00002f60| 68 65 20 78 79 2d 70 6c | 61 6e 65 2e 20 44 72 61 |he xy-pl|ane. Dra|
|00002f70| 67 67 69 6e 67 20 75 73 | 69 6e 67 20 41 44 4a 55 |gging us|ing ADJU|
|00002f80| 53 54 20 7a 6f 6f 6d 73 | 0a 20 20 20 20 20 20 20 |ST zooms|. |
|00002f90| 20 20 20 20 20 20 20 20 | 20 20 20 20 20 20 20 20 | | |
|00002fa0| 69 6e 2f 6f 75 74 20 28 | 69 2e 65 2e 20 69 74 20 |in/out (|i.e. it |
|00002fb0| 74 72 61 6e 73 6c 61 74 | 65 73 20 74 68 65 20 6d |translat|es the m|
|00002fc0| 6f 6c 65 63 75 6c 65 20 | 61 6c 6f 6e 67 20 74 68 |olecule |along th|
|00002fd0| 65 20 7a 2d 61 78 69 73 | 29 2e 0a 5a 2d 73 6c 61 |e z-axis|)..Z-sla|
|00002fe0| 62 20 6d 6f 64 65 3a 20 | 54 68 69 73 20 6f 6e 6c |b mode: |This onl|
|00002ff0| 79 20 68 61 73 20 61 20 | 76 69 73 69 62 6c 65 20 |y has a |visible |
|00003000| 65 66 66 65 63 74 20 69 | 66 20 74 68 65 20 22 7a |effect i|f the "z|
|00003010| 2d 73 6c 61 62 62 69 6e | 67 22 20 6f 70 74 69 6f |-slabbin|g" optio|
|00003020| 6e 20 69 73 20 74 69 63 | 6b 65 64 0a 20 20 20 20 |n is tic|ked. |
|00003030| 20 20 20 20 20 20 20 20 | 20 69 6e 20 74 68 65 20 | | in the |
|00003040| 22 4f 70 74 69 6f 6e 73 | 22 20 6d 65 6e 75 2e 20 |"Options|" menu. |
|00003050| 5a 2d 73 6c 61 62 62 69 | 6e 67 20 61 6c 6c 6f 77 |Z-slabbi|ng allow|
|00003060| 73 20 79 6f 75 20 74 6f | 20 73 65 65 20 22 69 6e |s you to| see "in|
|00003070| 73 69 64 65 22 20 74 68 | 65 0a 20 20 20 20 20 20 |side" th|e. |
|00003080| 20 20 20 20 20 20 20 6d | 6f 6c 65 63 75 6c 65 20 | m|olecule |
|00003090| 62 79 20 73 6c 61 62 62 | 69 6e 67 20 69 74 20 61 |by slabb|ing it a|
|000030a0| 67 61 69 6e 73 74 20 61 | 20 76 65 72 74 69 63 61 |gainst a| vertica|
|000030b0| 6c 20 70 6c 61 6e 65 2e | 20 54 68 65 20 73 6c 61 |l plane.| The sla|
|000030c0| 62 20 70 6c 61 6e 65 20 | 63 61 6e 0a 20 20 20 20 |b plane |can. |
|000030d0| 20 20 20 20 20 20 20 20 | 20 62 65 20 6d 6f 76 65 | | be move|
|000030e0| 64 20 61 6c 6f 6e 67 20 | 74 68 65 20 7a 2d 61 78 |d along |the z-ax|
|000030f0| 69 73 20 62 79 20 64 72 | 61 67 67 69 6e 67 20 77 |is by dr|agging w|
|00003100| 69 74 68 20 65 69 74 68 | 65 72 20 6d 6f 75 73 65 |ith eith|er mouse|
|00003110| 20 6b 65 79 2e 0a 44 69 | 74 68 65 72 20 74 6f 6f | key..Di|ther too|
|00003120| 6c 3a 20 53 65 65 20 6e | 65 78 74 20 70 61 73 73 |l: See n|ext pass|
|00003130| 61 67 65 0a 0a 20 44 69 | 73 70 6c 61 79 20 71 75 |age.. Di|splay qu|
|00003140| 61 6c 69 74 79 20 61 6e | 64 20 64 69 74 68 65 72 |ality an|d dither|
|00003150| 69 6e 67 0a 20 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |ing. ---|--------|
|00003160| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00003170| 2d 2d 0a 20 20 52 61 73 | 4d 6f 6c 20 70 72 6f 64 |--. Ras|Mol prod|
|00003180| 75 63 65 73 20 62 69 74 | 6d 61 70 73 20 77 69 74 |uces bit|maps wit|
|00003190| 68 20 32 35 36 20 63 6f | 6c 6f 75 72 20 70 61 6c |h 256 co|lour pal|
|000031a0| 65 74 74 65 73 2c 20 73 | 6f 20 74 68 65 79 20 64 |ettes, s|o they d|
|000031b0| 6f 20 6e 6f 74 20 64 69 | 73 70 6c 61 79 20 76 65 |o not di|splay ve|
|000031c0| 72 79 0a 77 65 6c 6c 20 | 69 6e 20 52 49 53 43 20 |ry.well |in RISC |
|000031d0| 4f 53 20 32 35 36 20 63 | 6f 6c 6f 75 72 20 6d 6f |OS 256 c|olour mo|
|000031e0| 64 65 73 20 77 69 74 68 | 20 74 68 65 20 73 74 61 |des with| the sta|
|000031f0| 6e 64 61 72 64 20 66 69 | 78 65 64 20 70 61 6c 65 |ndard fi|xed pale|
|00003200| 74 74 65 2e 20 49 6e 20 | 70 61 72 74 69 63 75 6c |tte. In |particul|
|00003210| 61 72 0a 73 70 61 63 65 | 20 66 69 6c 6c 69 6e 67 |ar.space| filling|
|00003220| 20 72 65 70 72 65 73 65 | 6e 74 61 74 69 6f 6e 73 | represe|ntations|
|00003230| 20 6c 6f 6f 6b 20 76 65 | 72 79 20 70 6f 6f 72 20 | look ve|ry poor |
|00003240| 69 6e 20 32 35 36 20 63 | 6f 6c 6f 75 72 20 6d 6f |in 256 c|olour mo|
|00003250| 64 65 73 2e 20 0a 20 0a | 20 20 54 68 65 72 65 66 |des. . .| Theref|
|00003260| 6f 72 65 20 74 68 65 20 | 52 49 53 43 20 4f 53 20 |ore the |RISC OS |
|00003270| 76 65 72 73 69 6f 6e 20 | 6f 66 20 52 61 73 4d 6f |version |of RasMo|
|00003280| 6c 20 69 73 20 61 62 6c | 65 20 74 6f 20 70 72 6f |l is abl|e to pro|
|00003290| 64 75 63 65 20 64 69 74 | 68 65 72 65 64 20 6f 75 |duce dit|hered ou|
|000032a0| 74 70 75 74 0a 75 73 69 | 6e 67 20 6d 6f 72 65 20 |tput.usi|ng more |
|000032b0| 6f 72 20 6c 65 73 73 20 | 74 68 65 20 73 61 6d 65 |or less |the same|
|000032c0| 20 61 6c 67 6f 72 69 74 | 68 6d 20 43 68 61 6e 67 | algorit|hm Chang|
|000032d0| 65 46 53 49 20 75 73 65 | 73 20 74 6f 20 64 69 74 |eFSI use|s to dit|
|000032e0| 68 65 72 20 69 6d 61 67 | 65 73 2e 20 54 68 69 73 |her imag|es. This|
|000032f0| 0a 74 61 6b 65 73 20 61 | 20 66 65 77 20 73 65 63 |.takes a| few sec|
|00003300| 6f 6e 64 73 2c 20 62 75 | 74 20 74 68 65 20 72 65 |onds, bu|t the re|
|00003310| 73 75 6c 74 73 20 61 72 | 65 20 77 6f 72 74 68 20 |sults ar|e worth |
|00003320| 77 68 69 6c 65 20 74 68 | 65 20 64 65 6c 61 79 2e |while th|e delay.|
|00003330| 20 44 69 74 68 65 72 69 | 6e 67 20 77 6f 72 6b 73 | Ditheri|ng works|
|00003340| 0a 69 6e 20 62 6f 74 68 | 20 32 35 36 20 61 6e 64 |.in both| 256 and|
|00003350| 20 31 36 20 63 6f 6c 6f | 75 72 20 6d 6f 64 65 73 | 16 colo|ur modes|
|00003360| 2e 20 41 73 20 64 69 74 | 68 65 72 69 6e 67 20 69 |. As dit|hering i|
|00003370| 73 20 71 75 69 74 65 20 | 74 69 6d 65 2d 63 6f 6e |s quite |time-con|
|00003380| 73 75 6d 69 6e 67 2c 20 | 69 74 20 69 73 20 6f 6e |suming, |it is on|
|00003390| 6c 79 0a 70 65 72 66 6f | 72 6d 65 64 20 6f 6e 20 |ly.perfo|rmed on |
|000033a0| 72 65 71 75 65 73 74 2c | 20 74 68 61 74 20 69 73 |request,| that is|
|000033b0| 20 69 66 20 79 6f 75 20 | 63 6c 69 63 6b 20 6f 6e | if you |click on|
|000033c0| 20 74 68 65 20 22 44 69 | 74 68 65 72 22 20 74 6f | the "Di|ther" to|
|000033d0| 6f 6c 20 28 74 68 65 20 | 62 6f 74 74 6f 6d 20 74 |ol (the |bottom t|
|000033e0| 6f 6f 6c 0a 6f 6e 20 74 | 68 65 20 74 6f 6f 6c 20 |ool.on t|he tool |
|000033f0| 62 61 72 29 2e 20 4f 66 | 20 63 6f 75 72 73 65 2c |bar). Of| course,|
|00003400| 20 61 73 20 73 6f 6f 6e | 20 61 73 20 74 68 65 20 | as soon| as the |
|00003410| 64 69 73 70 6c 61 79 20 | 63 68 61 6e 67 65 73 20 |display |changes |
|00003420| 28 65 2e 67 2e 20 62 65 | 63 61 75 73 65 20 79 6f |(e.g. be|cause yo|
|00003430| 75 0a 63 68 61 6e 67 65 | 20 61 20 64 69 73 70 6c |u.change| a displ|
|00003440| 61 79 20 6f 70 74 69 6f | 6e 20 6f 72 20 79 6f 75 |ay optio|n or you|
|00003450| 20 72 6f 74 61 74 65 20 | 74 68 65 20 6d 6f 6c 65 | rotate |the mole|
|00003460| 63 75 6c 65 29 2c 20 74 | 68 65 20 70 69 63 74 75 |cule), t|he pictu|
|00003470| 72 65 20 69 73 20 72 65 | 63 61 6c 63 75 6c 61 74 |re is re|calculat|
|00003480| 65 64 2c 0a 73 6f 20 69 | 74 20 68 61 73 20 74 6f |ed,.so i|t has to|
|00003490| 20 62 65 20 64 69 74 68 | 65 72 65 64 20 61 67 61 | be dith|ered aga|
|000034a0| 69 6e 2e 20 4e 6f 72 6d | 61 6c 6c 79 2c 20 79 6f |in. Norm|ally, yo|
|000034b0| 75 20 77 6f 75 6c 64 20 | 66 69 72 73 74 20 73 65 |u would |first se|
|000034c0| 74 20 61 6c 6c 20 74 68 | 65 20 6f 70 74 69 6f 6e |t all th|e option|
|000034d0| 73 20 79 6f 75 0a 77 61 | 6e 74 2c 20 65 2e 67 2e |s you.wa|nt, e.g.|
|000034e0| 20 22 53 70 61 63 65 66 | 69 6c 6c 22 20 61 6e 64 | "Spacef|ill" and|
|000034f0| 20 22 53 70 65 63 75 6c | 61 72 22 20 65 74 63 2e | "Specul|ar" etc.|
|00003500| 20 61 6e 64 20 74 68 65 | 6e 20 6f 6e 6c 79 20 77 | and the|n only w|
|00003510| 68 65 6e 20 65 76 65 72 | 79 74 68 69 6e 67 20 69 |hen ever|ything i|
|00003520| 73 0a 4f 4b 20 64 69 74 | 68 65 72 20 74 68 65 20 |s.OK dit|her the |
|00003530| 69 6d 61 67 65 20 66 6f | 72 20 66 69 6e 61 6c 20 |image fo|r final |
|00003540| 6f 75 74 70 75 74 2e 0a | 20 0a 20 20 4e 6f 74 65 |output..| . Note|
|00003550| 20 74 68 61 74 20 69 66 | 20 79 6f 75 20 73 75 62 | that if| you sub|
|00003560| 73 65 71 75 65 6e 74 6c | 79 20 73 61 76 65 20 74 |sequentl|y save t|
|00003570| 68 65 20 69 6d 61 67 65 | 20 61 73 20 61 20 73 70 |he image| as a sp|
|00003580| 72 69 74 65 2c 20 74 68 | 65 20 64 69 74 68 65 72 |rite, th|e dither|
|00003590| 65 64 20 76 65 72 73 69 | 6f 6e 0a 69 73 20 73 61 |ed versi|on.is sa|
|000035a0| 76 65 64 21 20 54 68 69 | 73 20 69 73 20 61 20 67 |ved! Thi|s is a g|
|000035b0| 6f 6f 64 20 6f 70 74 69 | 6f 6e 20 69 66 20 74 68 |ood opti|on if th|
|000035c0| 65 20 6d 61 69 6e 20 70 | 75 72 70 6f 73 65 20 6f |e main p|urpose o|
|000035d0| 66 20 74 68 65 20 70 69 | 63 74 75 72 65 20 69 73 |f the pi|cture is|
|000035e0| 20 74 6f 20 62 65 0a 76 | 69 65 77 65 64 2c 20 69 | to be.v|iewed, i|
|000035f0| 6e 20 70 61 72 74 69 63 | 75 6c 61 72 20 6f 6e 20 |n partic|ular on |
|00003600| 6d 61 63 68 69 6e 65 73 | 20 77 69 74 68 6f 75 74 |machines| without|
|00003610| 20 74 72 75 65 20 63 6f | 6c 6f 75 72 20 6d 6f 64 | true co|lour mod|
|00003620| 65 73 2e 20 49 66 20 68 | 6f 77 65 76 65 72 2c 20 |es. If h|owever, |
|00003630| 79 6f 75 0a 61 72 65 20 | 70 6c 61 6e 6e 69 6e 67 |you.are |planning|
|00003640| 20 74 6f 20 70 72 69 6e | 74 20 74 68 65 20 69 6d | to prin|t the im|
|00003650| 61 67 65 2c 20 79 6f 75 | 20 61 72 65 20 61 64 76 |age, you| are adv|
|00003660| 69 73 65 64 20 74 6f 20 | 73 61 76 65 20 74 68 65 |ised to |save the|
|00003670| 20 75 6e 64 69 74 68 65 | 72 65 64 0a 76 65 72 73 | undithe|red.vers|
|00003680| 69 6f 6e 20 28 79 6f 75 | 20 63 61 6e 20 72 65 76 |ion (you| can rev|
|00003690| 65 72 74 20 74 6f 20 74 | 68 65 20 75 6e 64 69 74 |ert to t|he undit|
|000036a0| 68 65 72 65 64 20 76 65 | 72 73 69 6f 6e 20 62 79 |hered ve|rsion by|
|000036b0| 20 63 68 6f 6f 73 69 6e | 67 20 22 52 65 63 61 6c | choosin|g "Recal|
|000036c0| 63 75 6c 61 74 65 22 0a | 66 72 6f 6d 20 74 68 65 |culate".|from the|
|000036d0| 20 6d 61 69 6e 20 6d 65 | 6e 75 29 2e 20 45 76 65 | main me|nu). Eve|
|000036e0| 6e 20 74 68 6f 75 67 68 | 20 74 68 69 73 20 6c 6f |n though| this lo|
|000036f0| 6f 6b 73 20 77 6f 72 73 | 65 20 6f 6e 20 73 63 72 |oks wors|e on scr|
|00003700| 65 65 6e 20 69 74 20 70 | 72 69 6e 74 73 20 6d 75 |een it p|rints mu|
|00003710| 63 68 20 62 65 74 74 65 | 72 0a 69 6e 20 70 61 72 |ch bette|r.in par|
|00003720| 74 69 63 75 6c 61 72 20 | 69 66 20 69 74 20 69 73 |ticular |if it is|
|00003730| 20 73 63 61 6c 65 64 20 | 62 65 66 6f 72 65 20 70 | scaled |before p|
|00003740| 72 69 6e 74 69 6e 67 21 | 0a 20 0a 20 20 54 6f 20 |rinting!|. . To |
|00003750| 63 6f 6d 70 61 72 65 20 | 52 61 73 4d 6f 6c 27 73 |compare |RasMol's|
|00003760| 20 69 6e 74 65 72 6e 61 | 6c 20 64 69 74 68 65 72 | interna|l dither|
|00003770| 69 6e 67 20 77 69 74 68 | 20 43 68 61 6e 67 65 46 |ing with| ChangeF|
|00003780| 53 49 2c 20 74 72 79 20 | 65 78 70 6f 72 74 69 6e |SI, try |exportin|
|00003790| 67 20 74 68 65 0a 75 6e | 64 69 74 68 65 72 65 64 |g the.un|dithered|
|000037a0| 20 73 70 72 69 74 65 20 | 28 77 68 69 63 68 20 63 | sprite |(which c|
|000037b0| 6f 6e 74 61 69 6e 73 20 | 61 20 66 75 6c 6c 20 32 |ontains |a full 2|
|000037c0| 35 36 20 63 6f 6c 6f 75 | 72 20 70 61 6c 65 74 74 |56 colou|r palett|
|000037d0| 65 29 20 61 6e 64 20 66 | 65 65 64 20 69 74 20 74 |e) and f|eed it t|
|000037e0| 68 72 6f 75 67 68 0a 43 | 68 61 6e 67 65 46 53 49 |hrough.C|hangeFSI|
|000037f0| 2e 0a 20 0a 20 54 68 65 | 72 65 20 61 72 65 20 73 |.. . The|re are s|
|00003800| 65 76 65 72 61 6c 20 6f | 74 68 65 72 20 77 61 79 |everal o|ther way|
|00003810| 73 20 6f 66 20 69 6d 70 | 72 6f 76 69 6e 67 20 6f |s of imp|roving o|
|00003820| 75 74 70 75 74 20 71 75 | 61 6c 69 74 79 3a 0a 20 |utput qu|ality:. |
|00003830| 31 29 20 66 6f 72 20 52 | 69 73 63 50 43 20 6f 77 |1) for R|iscPC ow|
|00003840| 6e 65 72 73 20 77 69 74 | 68 20 56 52 41 4d 3a 0a |ners wit|h VRAM:.|
|00003850| 20 20 20 20 2a 20 43 68 | 61 6e 67 65 20 74 6f 20 | * Ch|ange to |
|00003860| 61 20 33 32 37 36 38 20 | 63 6f 6c 6f 75 72 20 6d |a 32768 |colour m|
|00003870| 6f 64 65 0a 20 32 29 20 | 66 6f 72 20 6f 77 6e 65 |ode. 2) |for owne|
|00003880| 72 73 20 6f 66 20 61 20 | 43 43 20 43 6f 6c 6f 75 |rs of a |CC Colou|
|00003890| 72 43 61 72 64 3a 0a 20 | 20 20 20 2a 20 43 68 61 |rCard:. | * Cha|
|000038a0| 6e 67 65 20 74 68 65 20 | 32 35 36 20 63 6f 6c 6f |nge the |256 colo|
|000038b0| 75 72 20 70 61 6c 65 74 | 74 65 20 65 2e 67 2e 20 |ur palet|te e.g. |
|000038c0| 75 73 69 6e 67 20 74 68 | 65 20 22 50 61 6c 4d 61 |using th|e "PalMa|
|000038d0| 6b 65 72 22 20 75 74 69 | 6c 69 74 79 2e 20 54 68 |ker" uti|lity. Th|
|000038e0| 69 73 0a 20 20 20 20 20 | 20 67 69 76 65 73 20 74 |is. | gives t|
|000038f0| 68 65 20 73 61 6d 65 20 | 64 69 73 70 6c 61 79 20 |he same |display |
|00003900| 71 75 61 6c 69 74 79 20 | 61 73 20 61 20 31 36 20 |quality |as a 16 |
|00003910| 6d 69 6c 6c 6f 6e 20 63 | 6f 6c 6f 75 72 20 6d 6f |millon c|olour mo|
|00003920| 64 65 21 0a 20 33 29 20 | 2a 20 73 61 76 65 20 74 |de!. 3) |* save t|
|00003930| 68 65 20 73 70 72 69 74 | 65 20 61 6e 64 20 66 65 |he sprit|e and fe|
|00003940| 65 64 20 69 74 20 74 68 | 72 6f 75 67 68 20 43 68 |ed it th|rough Ch|
|00003950| 61 6e 67 65 46 53 49 20 | 61 73 20 73 75 67 67 65 |angeFSI |as sugge|
|00003960| 73 74 65 64 20 61 62 6f | 76 65 0a 0a 20 53 61 76 |sted abo|ve.. Sav|
|00003970| 69 6e 67 20 61 6e 64 20 | 65 78 70 6f 72 74 69 6e |ing and |exportin|
|00003980| 67 0a 20 2d 2d 2d 2d 2d | 2d 2d 2d 2d 0a 20 20 54 |g. -----|----. T|
|00003990| 68 65 20 63 75 72 72 65 | 6e 74 20 64 69 73 70 6c |he curre|nt displ|
|000039a0| 61 79 20 63 61 6e 20 62 | 65 20 73 61 76 65 64 20 |ay can b|e saved |
|000039b0| 61 73 20 61 20 73 70 72 | 69 74 65 20 75 73 69 6e |as a spr|ite usin|
|000039c0| 67 20 74 68 65 20 6d 65 | 6e 75 20 69 74 65 6d 20 |g the me|nu item |
|000039d0| 22 46 69 6c 65 2e 53 61 | 76 65 0a 73 70 72 69 74 |"File.Sa|ve.sprit|
|000039e0| 65 22 20 66 72 6f 6d 20 | 74 68 65 20 6d 61 69 6e |e" from |the main|
|000039f0| 20 6d 65 6e 75 2e 20 54 | 68 69 73 20 73 61 76 65 | menu. T|his save|
|00003a00| 73 20 74 68 65 20 69 6d | 61 67 65 20 61 73 20 61 |s the im|age as a|
|00003a10| 20 32 35 36 20 63 6f 6c | 6f 75 72 20 73 70 72 69 | 256 col|our spri|
|00003a20| 74 65 20 77 69 74 68 0a | 61 20 66 75 6c 6c 20 32 |te with.|a full 2|
|00003a30| 35 36 20 63 6f 6c 6f 75 | 72 20 70 61 6c 65 74 74 |56 colou|r palett|
|00003a40| 65 20 28 6e 6f 74 20 73 | 75 69 74 61 62 6c 65 20 |e (not s|uitable |
|00003a50| 66 6f 72 20 52 49 53 43 | 20 4f 53 20 32 20 75 6e |for RISC| OS 2 un|
|00003a60| 6c 65 73 73 20 79 6f 75 | 20 6c 6f 61 64 20 74 68 |less you| load th|
|00003a70| 65 0a 73 70 72 69 74 65 | 20 69 6e 74 6f 20 21 50 |e.sprite| into !P|
|00003a80| 61 69 6e 74 20 61 6e 64 | 20 72 65 6d 6f 76 65 20 |aint and| remove |
|00003a90| 74 68 65 20 70 61 6c 65 | 74 74 65 29 2e 20 49 66 |the pale|tte). If|
|00003aa0| 20 74 68 65 20 63 75 72 | 72 65 6e 74 6c 79 20 64 | the cur|rently d|
|00003ab0| 69 73 70 6c 61 79 65 64 | 20 69 6d 61 67 65 0a 69 |isplayed| image.i|
|00003ac0| 73 20 64 69 74 68 65 72 | 65 64 2c 20 74 68 65 20 |s dither|ed, the |
|00003ad0| 64 69 74 68 65 72 65 64 | 20 76 65 72 73 69 6f 6e |dithered| version|
|00003ae0| 20 69 73 20 73 61 76 65 | 64 2e 20 4e 6f 74 65 20 | is save|d. Note |
|00003af0| 74 68 61 74 20 69 74 20 | 69 73 20 6e 6f 74 20 70 |that it |is not p|
|00003b00| 6f 73 73 69 62 6c 65 20 | 74 6f 0a 73 61 76 65 20 |ossible |to.save |
|00003b10| 61 20 31 36 20 63 6f 6c | 6f 75 72 20 73 70 72 69 |a 16 col|our spri|
|00003b20| 74 65 2c 20 65 76 65 6e | 20 69 66 20 74 68 65 20 |te, even| if the |
|00003b30| 63 75 72 72 65 6e 74 20 | 69 6d 61 67 65 20 68 61 |current |image ha|
|00003b40| 73 20 62 65 65 6e 20 64 | 69 74 68 65 72 65 64 20 |s been d|ithered |
|00003b50| 74 6f 20 31 36 0a 63 6f | 6c 6f 75 72 73 2e 20 46 |to 16.co|lours. F|
|00003b60| 65 65 64 20 74 68 65 20 | 75 6e 64 69 74 68 65 72 |eed the |undither|
|00003b70| 65 64 20 69 6d 61 67 65 | 20 74 68 72 6f 75 67 68 |ed image| through|
|00003b80| 20 43 68 61 6e 67 65 46 | 53 49 20 74 6f 20 61 63 | ChangeF|SI to ac|
|00003b90| 68 69 65 76 65 20 74 68 | 69 73 20 65 66 66 65 63 |hieve th|is effec|
|00003ba0| 74 2e 0a 20 0a 20 20 22 | 46 69 6c 65 2e 45 78 70 |t.. . "|File.Exp|
|00003bb0| 6f 72 74 2e 47 49 46 22 | 20 61 6c 6c 6f 77 73 20 |ort.GIF"| allows |
|00003bc0| 79 6f 75 20 74 6f 20 73 | 61 76 65 20 74 68 65 20 |you to s|ave the |
|00003bd0| 63 75 72 72 65 6e 74 20 | 69 6d 61 67 65 20 28 6f |current |image (o|
|00003be0| 6e 6c 79 20 69 66 20 69 | 74 20 69 73 20 6e 6f 74 |nly if i|t is not|
|00003bf0| 0a 64 69 74 68 65 72 65 | 64 29 20 61 73 20 61 20 |.dithere|d) as a |
|00003c00| 32 35 36 20 63 6f 6c 6f | 75 72 20 47 49 46 20 66 |256 colo|ur GIF f|
|00003c10| 69 6c 65 20 77 69 74 68 | 20 61 20 32 35 36 20 63 |ile with| a 256 c|
|00003c20| 6f 6c 6f 75 72 20 70 61 | 6c 65 74 74 65 2e 0a 20 |olour pa|lette.. |
|00003c30| 0a 20 20 22 46 69 6c 65 | 2e 45 78 70 6f 72 74 2e |. "File|.Export.|
|00003c40| 45 50 53 20 28 62 69 74 | 6d 61 70 29 22 20 73 61 |EPS (bit|map)" sa|
|00003c50| 76 65 73 20 61 6e 20 45 | 50 53 20 66 69 6c 65 20 |ves an E|PS file |
|00003c60| 63 6f 6e 74 61 69 6e 69 | 6e 67 20 74 68 65 20 62 |containi|ng the b|
|00003c70| 69 74 6d 61 70 2e 0a 20 | 0a 20 20 22 46 69 6c 65 |itmap.. |. "File|
|00003c80| 2e 45 78 70 6f 72 74 2e | 56 65 63 74 6f 72 20 50 |.Export.|Vector P|
|00003c90| 53 22 20 69 73 20 61 20 | 76 65 72 79 20 70 6f 77 |S" is a |very pow|
|00003ca0| 65 72 66 75 6c 20 6f 70 | 74 69 6f 6e 20 77 68 69 |erful op|tion whi|
|00003cb0| 63 68 20 69 73 20 6e 6f | 74 20 66 75 6c 6c 79 0a |ch is no|t fully.|
|00003cc0| 69 6d 70 6c 65 6d 65 6e | 74 65 64 20 79 65 74 2e |implemen|ted yet.|
|00003cd0| 20 48 6f 77 65 76 65 72 | 2c 20 66 6f 72 20 73 6f | However|, for so|
|00003ce0| 6d 65 20 72 65 70 72 65 | 73 65 6e 74 61 74 69 6f |me repre|sentatio|
|00003cf0| 6e 73 20 69 74 20 73 68 | 6f 75 6c 64 20 77 6f 72 |ns it sh|ould wor|
|00003d00| 6b 20 61 6c 72 65 61 64 | 79 2e 0a 54 68 69 73 20 |k alread|y..This |
|00003d10| 6f 75 74 70 75 74 20 63 | 61 6e 20 62 65 20 66 65 |output c|an be fe|
|00003d20| 64 20 74 68 72 6f 75 67 | 68 20 61 20 50 6f 73 74 |d throug|h a Post|
|00003d30| 53 63 72 69 70 74 20 69 | 6e 74 65 72 70 72 65 74 |Script i|nterpret|
|00003d40| 65 72 2c 20 65 2e 67 2e | 20 52 69 53 63 72 69 70 |er, e.g.| RiScrip|
|00003d50| 74 20 74 6f 0a 70 72 6f | 64 75 63 65 20 61 20 44 |t to.pro|duce a D|
|00003d60| 72 61 77 66 69 6c 65 2e | 20 48 6f 77 65 76 65 72 |rawfile.| However|
|00003d70| 2c 20 64 6f 20 6e 6f 74 | 20 65 78 70 65 63 74 20 |, do not| expect |
|00003d80| 74 6f 6f 20 6d 75 63 68 | 2c 20 62 6f 74 68 20 76 |too much|, both v|
|00003d90| 65 63 74 6f 72 20 50 53 | 20 65 78 70 6f 72 74 0a |ector PS| export.|
|00003da0| 61 6e 64 20 52 69 53 63 | 72 69 70 74 20 61 72 65 |and RiSc|ript are|
|00003db0| 20 72 61 74 68 65 72 20 | 75 6e 73 74 61 62 6c 65 | rather |unstable|
|00003dc0| 20 73 74 69 6c 6c 2e 0a | 20 0a 20 43 6f 6e 66 69 | still..| . Confi|
|00003dd0| 67 75 72 61 74 69 6f 6e | 0a 20 2d 2d 2d 2d 2d 2d |guration|. ------|
|00003de0| 2d 2d 2d 2d 2d 2d 2d 0a | 20 20 52 61 73 4d 6f 6c |-------.| RasMol|
|00003df0| 20 70 72 6f 76 69 64 65 | 73 20 73 6f 6d 65 20 62 | provide|s some b|
|00003e00| 61 73 69 63 20 63 6f 6e | 66 69 67 75 72 61 74 69 |asic con|figurati|
|00003e10| 6f 6e 20 6f 70 74 69 6f | 6e 73 20 74 68 61 74 20 |on optio|ns that |
|00003e20| 63 61 6e 20 62 65 20 73 | 65 74 20 62 79 20 63 68 |can be s|et by ch|
|00003e30| 6f 6f 73 69 6e 67 0a 22 | 43 68 6f 69 63 65 73 22 |oosing."|Choices"|
|00003e40| 20 66 72 6f 6d 20 74 68 | 65 20 69 63 6f 6e 20 62 | from th|e icon b|
|00003e50| 61 72 20 6d 65 6e 75 2e | 0a 54 68 65 20 22 54 69 |ar menu.|.The "Ti|
|00003e60| 6d 65 20 73 6c 69 63 65 | 22 20 6f 70 74 69 6f 6e |me slice|" option|
|00003e70| 20 64 65 74 65 72 6d 69 | 6e 65 73 20 68 6f 77 20 | determi|nes how |
|00003e80| 6d 75 63 68 20 43 50 55 | 20 74 69 6d 65 20 74 68 |much CPU| time th|
|00003e90| 65 20 70 72 6f 67 72 61 | 6d 20 74 61 6b 65 73 2e |e progra|m takes.|
|00003ea0| 0a 44 65 63 72 65 61 73 | 69 6e 67 20 74 68 65 20 |.Decreas|ing the |
|00003eb0| 76 61 6c 75 65 20 6d 65 | 61 6e 73 20 74 68 61 74 |value me|ans that|
|00003ec0| 20 74 68 65 20 64 65 73 | 6b 74 6f 70 20 69 73 20 | the des|ktop is |
|00003ed0| 73 6c 6f 77 65 64 20 64 | 6f 77 6e 20 6c 65 73 73 |slowed d|own less|
|00003ee0| 2c 20 62 75 74 20 69 74 | 20 6d 61 79 0a 74 61 6b |, but it| may.tak|
|00003ef0| 65 20 6c 6f 6e 67 65 72 | 20 74 6f 20 63 61 6c 63 |e longer| to calc|
|00003f00| 75 6c 61 74 65 20 61 6e | 20 69 6d 61 67 65 2e 20 |ulate an| image. |
|00003f10| 49 6e 63 72 65 61 73 69 | 6e 67 20 74 68 65 20 76 |Increasi|ng the v|
|00003f20| 61 6c 75 65 20 6d 65 61 | 6e 73 20 74 68 61 74 20 |alue mea|ns that |
|00003f30| 6d 6f 72 65 0a 43 50 55 | 20 74 69 6d 65 20 69 73 |more.CPU| time is|
|00003f40| 20 74 61 6b 65 6e 2e 20 | 49 66 20 79 6f 75 20 65 | taken. |If you e|
|00003f50| 6e 74 65 72 20 30 2c 20 | 74 68 65 6e 20 6d 75 6c |nter 0, |then mul|
|00003f60| 74 69 74 61 73 6b 69 6e | 67 20 69 73 20 64 69 73 |titaskin|g is dis|
|00003f70| 61 62 6c 65 64 20 63 6f | 6d 70 6c 65 74 65 6c 79 |abled co|mpletely|
|00003f80| 0a 77 68 69 6c 65 20 69 | 6d 61 67 65 73 20 61 72 |.while i|mages ar|
|00003f90| 65 20 63 61 6c 63 75 6c | 61 74 65 64 2e 0a 20 0a |e calcul|ated.. .|
|00003fa0| 20 20 54 68 65 20 22 44 | 65 66 61 75 6c 74 20 73 | The "D|efault s|
|00003fb0| 63 61 6c 65 22 20 61 6e | 64 20 22 44 65 66 61 75 |cale" an|d "Defau|
|00003fc0| 6c 74 20 77 69 64 74 68 | 22 20 65 6e 74 72 69 65 |lt width|" entrie|
|00003fd0| 73 20 63 6f 72 72 65 73 | 70 6f 6e 64 20 74 6f 20 |s corres|pond to |
|00003fe0| 74 68 65 20 6d 65 6e 75 | 20 65 6e 74 72 69 65 73 |the menu| entries|
|00003ff0| 0a 6f 66 20 74 68 65 20 | 73 61 6d 65 20 6e 61 6d |.of the |same nam|
|00004000| 65 2e 20 54 68 65 79 20 | 63 61 6e 20 62 65 20 75 |e. They |can be u|
|00004010| 73 65 64 20 74 6f 20 73 | 65 74 20 74 68 65 20 76 |sed to s|et the v|
|00004020| 61 6c 75 65 73 20 74 6f | 20 62 65 20 75 73 65 64 |alues to| be used|
|00004030| 20 61 74 20 73 74 61 72 | 74 2d 75 70 0a 74 69 6d | at star|t-up.tim|
|00004040| 65 20 6f 66 20 74 68 65 | 20 70 72 6f 67 72 61 6d |e of the| program|
|00004050| 2e 20 4e 6f 74 65 20 74 | 68 61 74 20 61 20 73 6d |. Note t|hat a sm|
|00004060| 61 6c 6c 65 72 20 77 69 | 6e 64 6f 77 20 75 73 65 |aller wi|ndow use|
|00004070| 73 20 6c 65 73 73 20 6d | 65 6d 6f 72 79 2e 0a 20 |s less m|emory.. |
|00004080| 0a 20 20 4e 6f 74 65 20 | 74 68 61 74 20 69 66 20 |. Note |that if |
|00004090| 79 6f 75 20 64 69 73 61 | 62 6c 65 20 74 68 65 20 |you disa|ble the |
|000040a0| 74 6f 6f 6c 62 6f 78 20 | 62 79 20 64 65 73 65 6c |toolbox |by desel|
|000040b0| 65 63 74 69 6e 67 20 74 | 68 65 20 22 44 69 73 70 |ecting t|he "Disp|
|000040c0| 6c 61 79 20 74 6f 6f 6c | 62 6f 78 22 0a 6f 70 74 |lay tool|box".opt|
|000040d0| 69 6f 6e 2c 20 52 61 73 | 4d 6f 6c 20 72 65 76 65 |ion, Ras|Mol reve|
|000040e0| 72 74 73 20 74 6f 20 74 | 68 65 20 73 74 61 6e 64 |rts to t|he stand|
|000040f0| 61 72 64 20 69 6e 74 65 | 72 70 72 65 74 61 74 69 |ard inte|rpretati|
|00004100| 6f 6e 20 6f 66 20 6d 6f | 75 73 65 20 6f 70 65 72 |on of mo|use oper|
|00004110| 61 74 69 6f 6e 73 20 61 | 73 0a 75 73 65 64 20 62 |ations a|s.used b|
|00004120| 79 20 74 68 65 20 58 31 | 31 20 6f 72 20 4d 53 20 |y the X1|1 or MS |
|00004130| 57 69 6e 64 6f 77 73 20 | 76 65 72 73 69 6f 6e 3a |Windows |version:|
|00004140| 0a 20 0a 20 77 69 74 68 | 20 43 74 72 6c 20 68 65 |. . with| Ctrl he|
|00004150| 6c 64 20 64 6f 77 6e 3a | 20 20 7a 2d 73 6c 61 62 |ld down:| z-slab|
|00004160| 20 6d 6f 64 65 0a 20 77 | 69 74 68 20 53 68 69 66 | mode. w|ith Shif|
|00004170| 74 20 68 65 6c 64 20 64 | 6f 77 6e 3a 20 53 45 4c |t held d|own: SEL|
|00004180| 45 43 54 3a 20 72 6f 74 | 61 74 65 20 61 62 6f 75 |ECT: rot|ate abou|
|00004190| 74 20 7a 2d 61 78 69 73 | 0a 20 20 20 20 20 20 20 |t z-axis|. |
|000041a0| 20 20 20 20 20 20 20 20 | 20 20 20 20 20 20 20 20 | | |
|000041b0| 41 44 4a 55 53 54 3a 20 | 7a 6f 6f 6d 20 6d 6f 64 |ADJUST: |zoom mod|
|000041c0| 65 0a 20 65 6c 73 65 3a | 20 53 45 4c 45 43 54 3a |e. else:| SELECT:|
|000041d0| 20 74 72 61 6e 73 6c 61 | 74 65 20 69 6e 20 74 68 | transla|te in th|
|000041e0| 65 20 78 79 20 70 6c 61 | 6e 65 0a 20 20 20 20 20 |e xy pla|ne. |
|000041f0| 20 20 41 44 4a 55 53 54 | 3a 20 72 6f 74 61 74 65 | ADJUST|: rotate|
|00004200| 20 61 62 6f 75 74 20 78 | 2d 20 61 6e 64 20 79 2d | about x|- and y-|
|00004210| 61 78 65 73 0a 20 0a 20 | 53 61 76 69 6e 67 20 6d |axes. . |Saving m|
|00004220| 65 6d 6f 72 79 0a 20 2d | 2d 2d 2d 2d 2d 2d 2d 2d |emory. -|--------|
|00004230| 2d 2d 2d 2d 0a 20 20 52 | 61 73 4d 6f 6c 20 6a 75 |----. R|asMol ju|
|00004240| 73 74 20 61 62 6f 75 74 | 20 73 74 61 72 74 73 20 |st about| starts |
|00004250| 75 70 20 6f 6e 20 61 20 | 32 4d 42 20 6d 61 63 68 |up on a |2MB mach|
|00004260| 69 6e 65 2e 20 46 6f 72 | 20 74 68 65 20 66 69 72 |ine. For| the fir|
|00004270| 73 74 20 74 69 6d 65 2c | 20 79 6f 75 20 6d 69 67 |st time,| you mig|
|00004280| 68 74 0a 68 61 76 65 20 | 74 6f 20 64 6f 20 61 20 |ht.have |to do a |
|00004290| 63 6c 65 61 6e 20 62 6f | 6f 74 20 61 6e 64 20 73 |clean bo|ot and s|
|000042a0| 77 69 74 63 68 20 74 6f | 20 61 20 31 36 20 63 6f |witch to| a 16 co|
|000042b0| 6c 6f 75 72 20 6d 6f 64 | 65 20 62 65 66 6f 72 65 |lour mod|e before|
|000042c0| 20 52 61 73 4d 6f 6c 20 | 77 6f 75 6c 64 0a 73 74 | RasMol |would.st|
|000042d0| 61 72 74 2e 20 54 6f 20 | 73 61 76 65 20 6d 65 6d |art. To |save mem|
|000042e0| 6f 72 79 20 70 65 72 6d | 61 6e 65 6e 74 6c 79 2c |ory perm|anently,|
|000042f0| 20 72 65 64 75 63 65 20 | 74 68 65 20 77 69 6e 64 | reduce |the wind|
|00004300| 6f 77 20 73 69 7a 65 20 | 28 6e 6f 74 20 75 73 69 |ow size |(not usi|
|00004310| 6e 67 20 74 68 65 20 6d | 61 69 6e 0a 6d 65 6e 75 |ng the m|ain.menu|
|00004320| 2c 20 62 75 74 20 75 73 | 69 6e 67 20 74 68 65 20 |, but us|ing the |
|00004330| 69 63 6f 6e 62 61 72 20 | 22 43 68 6f 69 63 65 73 |iconbar |"Choices|
|00004340| 22 20 69 74 65 6d 29 20 | 61 6e 64 20 63 6c 69 63 |" item) |and clic|
|00004350| 6b 20 6f 6e 20 74 68 65 | 20 53 61 76 65 20 62 75 |k on the| Save bu|
|00004360| 74 74 6f 6e 2e 20 54 68 | 65 6e 0a 72 65 6c 6f 61 |tton. Th|en.reloa|
|00004370| 64 20 74 68 65 20 61 70 | 70 6c 69 63 61 74 69 6f |d the ap|plicatio|
|00004380| 6e 2e 20 4d 6f 73 74 20 | 6f 70 74 69 6f 6e 73 20 |n. Most |options |
|00004390| 64 6f 20 6e 6f 74 20 6e | 65 65 64 20 61 6e 79 20 |do not n|eed any |
|000043a0| 65 78 74 72 61 20 6d 65 | 6d 6f 72 79 20 61 6e 64 |extra me|mory and|
|000043b0| 20 6d 6f 73 74 0a 6d 6f | 6c 65 63 75 6c 65 73 20 | most.mo|lecules |
|000043c0| 61 72 65 20 72 61 74 68 | 65 72 20 73 6d 61 6c 6c |are rath|er small|
|000043d0| 2e 20 59 6f 75 20 73 68 | 6f 75 6c 64 20 68 6f 77 |. You sh|ould how|
|000043e0| 65 76 65 72 20 61 76 6f | 69 64 20 74 68 65 20 22 |ever avo|id the "|
|000043f0| 44 6f 74 20 73 75 72 66 | 61 63 65 22 20 6f 70 74 |Dot surf|ace" opt|
|00004400| 69 6f 6e 0a 61 73 20 74 | 68 69 73 20 74 61 6b 65 |ion.as t|his take|
|00004410| 73 20 6c 6f 74 73 20 6f | 66 20 65 78 74 72 61 20 |s lots o|f extra |
|00004420| 6d 65 6d 6f 72 79 2e 0a | 20 0a 20 53 63 72 69 70 |memory..| . Scrip|
|00004430| 74 20 66 69 6c 65 73 0a | 20 2d 2d 2d 2d 2d 2d 2d |t files.| -------|
|00004440| 2d 2d 2d 2d 2d 0a 20 20 | 53 63 72 69 70 74 20 66 |-----. |Script f|
|00004450| 69 6c 65 73 20 6d 61 79 | 20 63 6f 6e 74 61 69 6e |iles may| contain|
|00004460| 20 61 6e 20 61 72 62 69 | 74 72 61 72 79 20 6e 75 | an arbi|trary nu|
|00004470| 6d 62 65 72 20 6f 66 20 | 52 61 73 4d 6f 6c 20 63 |mber of |RasMol c|
|00004480| 6f 6d 6d 61 6e 64 73 2e | 20 46 6f 72 20 64 65 74 |ommands.| For det|
|00004490| 61 69 6c 73 0a 72 65 66 | 65 72 20 74 6f 20 74 68 |ails.ref|er to th|
|000044a0| 65 20 52 61 73 4d 6f 6c | 20 6d 61 6e 75 61 6c 2e |e RasMol| manual.|
|000044b0| 20 53 63 72 69 70 74 20 | 66 69 6c 65 73 20 6d 75 | Script |files mu|
|000044c0| 73 74 20 68 61 76 65 20 | 74 68 65 20 66 69 6c 65 |st have |the file|
|000044d0| 20 74 79 70 65 20 22 52 | 61 73 4d 6f 6c 53 63 22 | type "R|asMolSc"|
|000044e0| 0a 69 6e 20 6f 72 64 65 | 72 20 74 6f 20 62 65 20 |.in orde|r to be |
|000044f0| 72 65 63 6f 67 6e 69 73 | 65 64 20 62 79 20 52 61 |recognis|ed by Ra|
|00004500| 73 4d 6f 6c 2e 20 44 6f | 75 62 6c 65 2d 63 6c 69 |sMol. Do|uble-cli|
|00004510| 63 6b 69 6e 67 20 6f 6e | 20 61 20 73 63 72 69 70 |cking on| a scrip|
|00004520| 74 20 66 69 6c 65 20 6f | 72 0a 64 72 61 67 67 69 |t file o|r.draggi|
|00004530| 6e 67 20 69 74 20 74 6f | 20 6f 6e 65 20 6f 66 20 |ng it to| one of |
|00004540| 74 68 65 20 52 61 73 4d | 6f 6c 20 77 69 6e 64 6f |the RasM|ol windo|
|00004550| 77 73 20 73 74 61 72 74 | 73 20 74 68 65 20 73 63 |ws start|s the sc|
|00004560| 72 69 70 74 2e 20 53 63 | 72 69 70 74 73 20 64 6f |ript. Sc|ripts do|
|00004570| 20 6e 6f 74 0a 6d 75 6c | 74 69 74 61 73 6b 2c 20 | not.mul|titask, |
|00004580| 62 75 74 20 79 6f 75 20 | 63 61 6e 20 61 62 6f 72 |but you |can abor|
|00004590| 74 20 74 68 65 6d 20 62 | 79 20 70 72 65 73 73 69 |t them b|y pressi|
|000045a0| 6e 67 20 61 6e 64 20 68 | 6f 6c 64 69 6e 67 20 64 |ng and h|olding d|
|000045b0| 6f 77 6e 20 74 68 65 20 | 45 73 63 61 70 65 20 6b |own the |Escape k|
|000045c0| 65 79 0a 75 6e 74 69 6c | 20 74 68 65 20 68 6f 75 |ey.until| the hou|
|000045d0| 72 67 6c 61 73 73 20 64 | 69 73 61 70 70 65 61 72 |rglass d|isappear|
|000045e0| 73 2e 0a 20 20 41 20 73 | 63 72 69 70 74 20 66 69 |s.. A s|cript fi|
|000045f0| 6c 65 20 77 68 69 63 68 | 20 72 65 70 72 6f 64 75 |le which| reprodu|
|00004600| 63 65 73 20 74 68 65 20 | 63 75 72 72 65 6e 74 20 |ces the |current |
|00004610| 73 65 74 75 70 20 63 61 | 6e 20 62 65 20 73 61 76 |setup ca|n be sav|
|00004620| 65 64 20 75 73 69 6e 67 | 20 74 68 65 0a 22 46 69 |ed using| the."Fi|
|00004630| 6c 65 2e 53 61 76 65 20 | 73 63 72 69 70 74 22 20 |le.Save |script" |
|00004640| 6d 65 6e 75 20 69 74 65 | 6d 2e 20 49 74 20 64 6f |menu ite|m. It do|
|00004650| 65 73 20 6e 6f 74 20 69 | 6e 63 6c 75 64 65 20 61 |es not i|nclude a|
|00004660| 6c 6c 20 6f 70 74 69 6f | 6e 73 2c 20 65 2e 67 2e |ll optio|ns, e.g.|
|00004670| 20 74 68 65 20 22 44 6f | 74 0a 73 75 72 66 61 63 | the "Do|t.surfac|
|00004680| 65 22 20 6f 70 74 69 6f | 6e 20 69 73 20 69 67 6e |e" optio|n is ign|
|00004690| 6f 72 65 64 2e 20 48 6f | 77 65 76 65 72 2c 20 69 |ored. Ho|wever, i|
|000046a0| 74 20 69 73 20 61 20 67 | 6f 6f 64 20 70 6f 69 6e |t is a g|ood poin|
|000046b0| 74 20 74 6f 20 73 74 61 | 72 74 20 66 72 6f 6d 20 |t to sta|rt from |
|000046c0| 69 66 20 79 6f 75 0a 77 | 61 6e 74 20 74 6f 20 62 |if you.w|ant to b|
|000046d0| 65 20 61 62 6c 65 20 74 | 6f 20 72 65 73 74 6f 72 |e able t|o restor|
|000046e0| 65 20 61 20 63 65 72 74 | 61 69 6e 20 73 65 74 20 |e a cert|ain set |
|000046f0| 6f 66 20 6f 70 74 69 6f | 6e 73 20 6c 61 74 65 72 |of optio|ns later|
|00004700| 2e 0a 20 20 4e 6f 74 65 | 20 74 68 61 74 20 75 73 |.. Note| that us|
|00004710| 69 6e 67 20 73 63 72 69 | 70 74 73 20 79 6f 75 20 |ing scri|pts you |
|00004720| 63 61 6e 20 70 72 6f 64 | 75 63 65 20 72 75 6e 6e |can prod|uce runn|
|00004730| 69 6e 67 20 64 65 6d 6f | 6e 73 74 72 61 74 69 6f |ing demo|nstratio|
|00004740| 6e 73 3a 20 55 73 65 20 | 74 68 65 0a 72 65 66 72 |ns: Use |the.refr|
|00004750| 65 73 68 20 63 6f 6d 6d | 61 6e 64 20 74 6f 20 66 |esh comm|and to f|
|00004760| 6f 72 63 65 20 74 68 65 | 20 73 63 72 65 65 6e 20 |orce the| screen |
|00004770| 74 6f 20 62 65 20 75 70 | 64 61 74 65 64 20 77 68 |to be up|dated wh|
|00004780| 69 6c 65 20 74 68 65 20 | 73 63 72 69 70 74 20 69 |ile the |script i|
|00004790| 73 20 72 75 6e 6e 69 6e | 67 2e 0a 54 68 65 20 70 |s runnin|g..The p|
|000047a0| 61 75 73 65 20 63 6f 6d | 6d 61 6e 64 20 63 61 6e |ause com|mand can|
|000047b0| 20 62 65 20 75 73 65 64 | 20 74 6f 20 61 73 6b 20 | be used| to ask |
|000047c0| 74 68 65 20 75 73 65 72 | 20 74 6f 20 70 72 65 73 |the user| to pres|
|000047d0| 73 20 61 20 6b 65 79 20 | 74 6f 20 67 6f 20 6f 6e |s a key |to go on|
|000047e0| 2e 20 57 68 65 6e 0a 64 | 6f 69 6e 67 20 73 6f 20 |. When.d|oing so |
|000047f0| 69 74 20 69 73 20 61 64 | 76 69 73 61 62 6c 65 20 |it is ad|visable |
|00004800| 74 6f 20 75 73 65 20 74 | 68 65 20 65 63 68 6f 20 |to use t|he echo |
|00004810| 63 6f 6d 6d 61 6e 64 20 | 74 6f 20 70 72 69 6e 74 |command |to print|
|00004820| 20 73 6f 6d 65 20 74 65 | 78 74 20 69 6e 20 74 68 | some te|xt in th|
|00004830| 65 0a 63 6f 6d 6d 61 6e | 64 20 77 69 6e 64 6f 77 |e.comman|d window|
|00004840| 20 6c 69 6b 65 20 22 50 | 72 65 73 73 20 61 6e 79 | like "P|ress any|
|00004850| 20 6b 65 79 20 74 6f 20 | 67 6f 20 6f 6e 22 2e 0a | key to |go on"..|
|00004860| 20 0a 20 50 43 20 73 63 | 72 69 70 74 20 64 69 72 | . PC sc|ript dir|
|00004870| 65 63 74 6f 72 69 65 73 | 0a 20 2d 2d 2d 2d 2d 2d |ectories|. ------|
|00004880| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 0a |--------|-------.|
|00004890| 20 20 53 6f 6d 65 20 70 | 65 6f 70 6c 65 20 68 61 | Some p|eople ha|
|000048a0| 76 65 20 62 75 69 6c 74 | 20 73 63 72 69 70 74 20 |ve built| script |
|000048b0| 64 69 72 65 63 74 6f 72 | 69 65 73 20 77 68 69 63 |director|ies whic|
|000048c0| 68 20 63 6f 6e 74 61 69 | 6e 20 6d 6f 6c 65 63 75 |h contai|n molecu|
|000048d0| 6c 65 20 66 69 6c 65 73 | 20 61 6e 64 0a 73 63 72 |le files| and.scr|
|000048e0| 69 70 74 73 2e 20 55 73 | 75 61 6c 6c 79 2c 20 74 |ipts. Us|ually, t|
|000048f0| 68 65 72 65 20 69 73 20 | 6f 6e 65 20 6d 61 69 6e |here is |one main|
|00004900| 20 65 6e 74 72 79 20 73 | 63 72 69 70 74 20 74 6f | entry s|cript to|
|00004910| 20 62 65 20 73 74 61 72 | 74 65 64 20 63 61 6c 6c | be star|ted call|
|00004920| 65 64 0a 73 6f 6d 65 74 | 68 69 6e 67 2e 54 4f 50 |ed.somet|hing.TOP|
|00004930| 2e 20 4f 6e 20 74 68 65 | 20 50 43 20 70 6c 61 74 |. On the| PC plat|
|00004940| 66 6f 72 6d 20 79 6f 75 | 20 77 6f 75 6c 64 20 63 |form you| would c|
|00004950| 68 61 6e 67 65 20 74 68 | 65 20 63 75 72 72 65 6e |hange th|e curren|
|00004960| 74 20 64 69 72 65 63 74 | 6f 72 79 20 74 6f 0a 74 |t direct|ory to.t|
|00004970| 68 65 20 73 63 72 69 70 | 74 20 64 69 72 65 63 74 |he scrip|t direct|
|00004980| 6f 72 79 20 61 6e 64 20 | 74 68 65 6e 20 72 75 6e |ory and |then run|
|00004990| 20 74 68 65 20 73 63 72 | 69 70 74 2e 20 54 68 69 | the scr|ipt. Thi|
|000049a0| 73 20 77 61 79 2c 20 74 | 68 65 20 73 63 72 69 70 |s way, t|he scrip|
|000049b0| 74 20 63 61 6e 0a 72 65 | 66 65 72 65 6e 63 65 20 |t can.re|ference |
|000049c0| 74 68 65 20 6d 6f 6c 65 | 63 75 6c 65 20 66 69 6c |the mole|cule fil|
|000049d0| 65 73 20 77 69 74 68 6f | 75 74 20 61 6e 79 20 70 |es witho|ut any p|
|000049e0| 61 74 68 6e 61 6d 65 20 | 62 75 74 20 73 69 6d 70 |athname |but simp|
|000049f0| 6c 79 20 62 79 20 73 70 | 65 63 69 66 79 69 6e 67 |ly by sp|ecifying|
|00004a00| 0a 74 68 65 69 72 20 6e | 61 6d 65 2e 0a 49 6e 20 |.their n|ame..In |
|00004a10| 6f 72 64 65 72 20 74 6f | 20 6d 61 6b 65 20 70 6f |order to| make po|
|00004a20| 72 74 69 6e 67 20 6f 66 | 20 74 68 65 73 65 20 64 |rting of| these d|
|00004a30| 69 72 65 63 74 6f 72 69 | 65 73 20 65 61 73 69 65 |irectori|es easie|
|00004a40| 72 2c 20 52 61 73 4d 6f | 6c 20 70 72 6f 76 69 64 |r, RasMo|l provid|
|00004a50| 65 73 20 74 68 65 0a 66 | 6f 6c 6c 6f 77 69 6e 67 |es the.f|ollowing|
|00004a60| 20 66 65 61 74 75 72 65 | 73 3a 0a 2d 20 61 75 74 | feature|s:.- aut|
|00004a70| 6f 6d 61 74 69 63 20 63 | 6f 6e 76 65 72 73 69 6f |omatic c|onversio|
|00004a80| 6e 20 6f 66 20 50 43 20 | 66 69 6c 65 6e 61 6d 65 |n of PC |filename|
|00004a90| 73 20 74 6f 20 41 63 6f | 72 6e 20 66 69 6c 65 6e |s to Aco|rn filen|
|00004aa0| 61 6d 65 73 2c 20 65 2e | 67 2e 20 61 20 63 6f 6d |ames, e.|g. a com|
|00004ab0| 6d 61 6e 64 0a 20 20 22 | 6c 6f 61 64 20 44 4e 41 |mand. "|load DNA|
|00004ac0| 2e 50 44 42 22 20 69 73 | 20 61 75 74 6f 6d 61 74 |.PDB" is| automat|
|00004ad0| 69 63 61 6c 6c 79 20 63 | 6f 6e 76 65 72 74 65 64 |ically c|onverted|
|00004ae0| 20 74 6f 20 22 6c 6f 61 | 64 20 44 4e 41 2f 50 44 | to "loa|d DNA/PD|
|00004af0| 42 22 2e 0a 2d 20 69 66 | 20 61 20 66 69 6c 65 20 |B"..- if| a file |
|00004b00| 69 73 20 6e 6f 74 20 66 | 6f 75 6e 64 2c 20 52 61 |is not f|ound, Ra|
|00004b10| 73 4d 6f 6c 20 6c 6f 6f | 6b 73 20 69 6e 73 69 64 |sMol loo|ks insid|
|00004b20| 65 20 74 68 65 20 64 69 | 72 65 63 74 6f 72 79 20 |e the di|rectory |
|00004b30| 73 70 65 63 69 66 69 65 | 64 20 62 79 0a 20 20 74 |specifie|d by. t|
|00004b40| 68 65 20 73 79 73 74 65 | 6d 20 76 61 72 69 61 62 |he syste|m variab|
|00004b50| 6c 65 20 52 61 73 4d 6f | 6c 24 46 69 6c 65 44 69 |le RasMo|l$FileDi|
|00004b60| 72 0a 53 6f 20 61 6c 6c | 20 79 6f 75 20 68 61 76 |r.So all| you hav|
|00004b70| 65 20 74 6f 20 64 6f 20 | 69 73 20 74 6f 20 67 69 |e to do |is to gi|
|00004b80| 76 65 20 74 68 65 20 6d | 61 69 6e 20 73 63 72 69 |ve the m|ain scri|
|00004b90| 70 74 20 66 69 6c 65 20 | 28 74 68 65 20 6f 6e 65 |pt file |(the one|
|00004ba0| 20 65 6e 64 69 6e 67 20 | 69 6e 0a 2f 54 4f 50 29 | ending |in./TOP)|
|00004bb0| 20 74 68 65 20 63 6f 72 | 72 65 63 74 20 74 79 70 | the cor|rect typ|
|00004bc0| 65 20 22 52 61 73 4d 6f | 6c 53 63 22 20 61 6e 64 |e "RasMo|lSc" and|
|00004bd0| 20 61 64 64 20 61 20 21 | 52 75 6e 20 66 69 6c 65 | add a !|Run file|
|00004be0| 20 74 6f 20 74 68 65 20 | 64 69 72 65 63 74 6f 72 | to the |director|
|00004bf0| 79 20 77 68 69 63 68 0a | 72 65 61 64 73 20 61 73 |y which.|reads as|
|00004c00| 20 66 6f 6c 6c 6f 77 73 | 3a 0a 20 0a 20 53 65 74 | follows|:. . Set|
|00004c10| 20 52 61 73 4d 6f 6c 24 | 46 69 6c 65 44 69 72 20 | RasMol$|FileDir |
|00004c20| 3c 4f 62 65 79 24 44 69 | 72 3e 0a 20 46 69 6c 65 |<Obey$Di|r>. File|
|00004c30| 72 5f 52 75 6e 20 2a 2f | 54 4f 50 0a 0a 28 6f 72 |r_Run */|TOP..(or|
|00004c40| 2c 20 69 66 20 74 68 65 | 72 65 20 61 72 65 20 73 |, if the|re are s|
|00004c50| 65 76 65 72 61 6c 20 66 | 69 6c 65 73 20 65 6e 64 |everal f|iles end|
|00004c60| 69 6e 67 20 69 6e 20 2f | 54 4f 50 2c 20 71 75 6f |ing in /|TOP, quo|
|00004c70| 74 65 20 74 68 65 20 6e | 61 6d 65 20 6f 66 20 74 |te the n|ame of t|
|00004c80| 68 65 20 66 69 6c 65 0a | 79 6f 75 20 77 61 6e 74 |he file.|you want|
|00004c90| 20 74 6f 20 62 65 20 72 | 75 6e 2c 20 65 2e 67 2e | to be r|un, e.g.|
|00004ca0| 20 46 69 6c 65 72 5f 52 | 75 6e 20 44 4e 41 2f 54 | Filer_R|un DNA/T|
|00004cb0| 4f 50 29 0a 20 0a 44 6f | 75 62 6c 65 2d 63 6c 69 |OP). .Do|uble-cli|
|00004cc0| 63 6b 69 6e 67 20 6f 6e | 20 74 68 65 20 21 52 75 |cking on| the !Ru|
|00004cd0| 6e 20 66 69 6c 65 20 73 | 65 74 73 20 75 70 20 74 |n file s|ets up t|
|00004ce0| 68 65 20 76 61 72 69 61 | 62 6c 65 20 61 6e 64 20 |he varia|ble and |
|00004cf0| 73 74 61 72 74 73 20 74 | 68 65 20 73 63 72 69 70 |starts t|he scrip|
|00004d00| 74 2e 0a 49 66 20 79 6f | 75 20 74 75 72 6e 20 74 |t..If yo|u turn t|
|00004d10| 68 65 20 73 63 72 69 70 | 74 20 64 69 72 65 63 74 |he scrip|t direct|
|00004d20| 6f 72 79 20 69 6e 20 61 | 6e 20 61 70 70 6c 69 63 |ory in a|n applic|
|00004d30| 61 74 69 6f 6e 20 62 79 | 20 67 69 76 69 6e 67 20 |ation by| giving |
|00004d40| 69 74 20 61 20 6e 61 6d | 65 20 73 74 61 72 74 69 |it a nam|e starti|
|00004d50| 6e 67 0a 77 69 74 68 20 | 27 21 27 2c 20 79 6f 75 |ng.with |'!', you|
|00004d60| 20 63 61 6e 20 65 76 65 | 6e 20 64 6f 75 62 6c 65 | can eve|n double|
|00004d70| 2d 63 6c 69 63 6b 20 6f | 6e 20 74 68 65 20 64 69 |-click o|n the di|
|00004d80| 72 65 63 74 6f 72 79 2e | 20 53 63 72 69 70 74 20 |rectory.| Script |
|00004d90| 64 69 72 65 63 74 6f 72 | 69 65 73 20 61 72 65 0a |director|ies are.|
|00004da0| 61 76 61 69 6c 61 62 6c | 65 20 66 72 6f 6d 20 74 |availabl|e from t|
|00004db0| 68 65 20 57 57 57 20 68 | 6f 6d 65 20 70 61 67 65 |he WWW h|ome page|
|00004dc0| 20 28 73 65 65 20 62 65 | 6c 6f 77 20 22 4c 69 6e | (see be|low "Lin|
|00004dd0| 6b 73 20 74 6f 20 6d 6f | 6c 65 63 75 6c 65 20 64 |ks to mo|lecule d|
|00004de0| 61 74 61 62 61 6e 6b 73 | 20 61 6e 64 20 57 57 57 |atabanks| and WWW|
|00004df0| 0a 70 61 67 65 73 20 61 | 62 6f 75 74 20 52 61 73 |.pages a|bout Ras|
|00004e00| 4d 6f 6c 22 29 2e 0a 0a | 20 44 69 73 70 6c 61 79 |Mol")...| Display|
|00004e10| 20 74 79 70 65 73 0a 20 | 2d 2d 2d 2d 2d 2d 2d 2d | types. |--------|
|00004e20| 2d 2d 2d 2d 2d 0a 20 20 | 57 68 65 6e 20 6c 6f 61 |-----. |When loa|
|00004e30| 64 65 64 2c 20 61 20 6d | 6f 6c 65 63 75 6c 65 20 |ded, a m|olecule |
|00004e40| 69 73 20 64 69 73 70 6c | 61 79 65 64 20 69 6e 20 |is displ|ayed in |
|00004e50| 57 69 72 65 66 72 61 6d | 65 20 6d 6f 64 65 2e 20 |Wirefram|e mode. |
|00004e60| 54 6f 20 63 68 61 6e 67 | 65 20 74 68 65 0a 64 69 |To chang|e the.di|
|00004e70| 73 70 6c 61 79 20 6d 6f | 64 65 2c 20 62 72 69 6e |splay mo|de, brin|
|00004e80| 67 20 75 70 20 74 68 65 | 20 6d 61 69 6e 20 4d 65 |g up the| main Me|
|00004e90| 6e 75 20 62 79 20 70 72 | 65 73 73 69 6e 67 20 74 |nu by pr|essing t|
|00004ea0| 68 65 20 6d 69 64 64 6c | 65 20 6d 6f 75 73 65 20 |he middl|e mouse |
|00004eb0| 62 75 74 74 6f 6e 20 6f | 76 65 72 0a 74 68 65 20 |button o|ver.the |
|00004ec0| 4d 6f 6c 65 63 75 6c 65 | 20 77 69 6e 64 6f 77 2e |Molecule| window.|
|00004ed0| 20 46 72 6f 6d 20 74 68 | 65 20 22 44 69 73 70 6c | From th|e "Displ|
|00004ee0| 61 79 22 20 73 75 62 6d | 65 6e 75 20 79 6f 75 20 |ay" subm|enu you |
|00004ef0| 63 61 6e 20 63 68 6f 6f | 73 65 20 79 6f 75 72 20 |can choo|se your |
|00004f00| 70 72 65 66 65 72 72 65 | 64 0a 64 69 73 70 6c 61 |preferre|d.displa|
|00004f10| 79 20 73 74 79 6c 65 20 | 66 72 6f 6d 20 74 68 65 |y style |from the|
|00004f20| 20 66 6f 6c 6c 6f 77 69 | 6e 67 3a 0a 20 2d 20 57 | followi|ng:. - W|
|00004f30| 69 72 65 66 72 61 6d 65 | 20 20 20 20 20 20 20 20 |ireframe| |
|00004f40| 20 2d 20 42 61 6c 6c 26 | 53 74 69 63 6b 0a 20 2d | - Ball&|Stick. -|
|00004f50| 20 42 61 63 6b 62 6f 6e | 65 20 20 20 20 20 20 20 | Backbon|e |
|00004f60| 20 20 20 2d 20 52 69 62 | 62 6f 6e 73 0a 20 2d 20 | - Rib|bons. - |
|00004f70| 53 74 69 63 6b 73 20 20 | 20 20 20 20 20 20 20 20 |Sticks | |
|00004f80| 20 20 2d 20 53 74 72 61 | 6e 64 73 0a 20 2d 20 53 | - Stra|nds. - S|
|00004f90| 70 61 63 65 66 69 6c 6c | 20 20 20 20 20 20 20 20 |pacefill| |
|00004fa0| 20 2d 20 43 61 72 74 6f | 6f 6e 73 0a 20 54 68 65 | - Carto|ons. The|
|00004fb0| 20 64 65 66 61 75 6c 74 | 20 69 73 20 57 69 72 65 | default| is Wire|
|00004fc0| 66 72 61 6d 65 2e 20 54 | 68 69 73 20 69 73 20 61 |frame. T|his is a|
|00004fd0| 6c 73 6f 20 74 68 65 20 | 66 61 73 74 65 73 74 20 |lso the |fastest |
|00004fe0| 77 61 79 20 6f 66 20 64 | 69 73 70 6c 61 79 69 6e |way of d|isplayin|
|00004ff0| 67 20 74 68 65 20 6d 6f | 6c 65 63 75 6c 65 2e 0a |g the mo|lecule..|
|00005000| 55 73 65 20 74 68 69 73 | 20 73 74 79 6c 65 20 69 |Use this| style i|
|00005010| 66 20 79 6f 75 20 77 61 | 6e 74 20 74 6f 20 74 72 |f you wa|nt to tr|
|00005020| 61 6e 73 6c 61 74 65 2f | 72 6f 74 61 74 65 20 74 |anslate/|rotate t|
|00005030| 68 65 20 6d 6f 6c 65 63 | 75 6c 65 20 61 20 6c 6f |he molec|ule a lo|
|00005040| 74 2c 20 61 73 20 74 68 | 65 73 65 20 6f 70 65 72 |t, as th|ese oper|
|00005050| 61 74 69 6f 6e 73 0a 77 | 6f 72 6b 20 69 6e 20 72 |ations.w|ork in r|
|00005060| 65 61 6c 20 74 69 6d 65 | 20 69 6e 20 57 69 72 65 |eal time| in Wire|
|00005070| 66 72 61 6d 65 20 6d 6f | 64 65 2e 0a 20 54 68 65 |frame mo|de.. The|
|00005080| 20 73 75 62 2d 6d 65 6e | 75 20 6f 66 20 22 57 69 | sub-men|u of "Wi|
|00005090| 72 65 66 72 61 6d 65 22 | 20 6c 65 74 73 20 79 6f |reframe"| lets yo|
|000050a0| 75 20 74 6f 20 63 68 6f | 6f 73 65 20 73 6f 6c 69 |u to cho|ose soli|
|000050b0| 64 20 6f 72 20 64 61 73 | 68 65 64 20 6c 69 6e 65 |d or das|hed line|
|000050c0| 73 20 28 74 68 65 20 22 | 64 61 73 68 65 64 22 0a |s (the "|dashed".|
|000050d0| 69 74 65 6d 20 69 73 20 | 61 20 73 68 6f 72 74 63 |item is |a shortc|
|000050e0| 75 74 20 66 6f 72 20 74 | 68 65 20 22 77 69 72 65 |ut for t|he "wire|
|000050f0| 66 72 61 6d 65 20 64 61 | 73 68 22 20 63 6f 6d 6d |frame da|sh" comm|
|00005100| 61 6e 64 29 2e 0a 20 54 | 68 65 20 73 75 62 2d 6d |and).. T|he sub-m|
|00005110| 65 6e 75 20 6f 66 20 22 | 53 74 69 63 6b 73 22 20 |enu of "|Sticks" |
|00005120| 61 6c 6c 6f 77 73 20 79 | 6f 75 20 74 6f 20 65 6e |allows y|ou to en|
|00005130| 74 65 72 20 74 68 65 20 | 74 68 69 63 6b 6e 65 73 |ter the |thicknes|
|00005140| 73 20 6f 66 20 74 68 65 | 20 73 74 69 63 6b 73 2e |s of the| sticks.|
|00005150| 20 50 72 65 73 73 69 6e | 67 0a 22 44 65 66 61 75 | Pressin|g."Defau|
|00005160| 6c 74 22 20 66 69 6c 6c | 73 20 69 6e 20 74 68 65 |lt" fill|s in the|
|00005170| 20 64 65 66 61 75 6c 74 | 20 76 61 6c 75 65 20 28 | default| value (|
|00005180| 77 68 69 63 68 20 69 73 | 20 34 30 2c 20 6f 72 20 |which is| 40, or |
|00005190| 38 30 20 69 66 20 74 68 | 65 20 6d 6f 6c 65 63 75 |80 if th|e molecu|
|000051a0| 6c 65 20 68 61 73 20 6d | 6f 72 65 20 74 68 61 6e |le has m|ore than|
|000051b0| 0a 32 35 36 20 61 74 6f | 6d 73 29 2e 0a 20 0a 20 |.256 ato|ms).. . |
|000051c0| 46 6f 72 20 6d 6f 72 65 | 20 64 65 74 61 69 6c 73 |For more| details|
|000051d0| 20 6f 6e 20 74 68 65 73 | 65 20 73 74 79 6c 65 73 | on thes|e styles|
|000051e0| 2c 20 74 79 70 65 20 22 | 68 65 6c 70 20 3c 64 69 |, type "|help <di|
|000051f0| 73 70 6c 61 79 20 73 74 | 79 6c 65 3e 22 20 6f 6e |splay st|yle>" on|
|00005200| 20 74 68 65 20 52 61 73 | 4d 6f 6c 0a 63 6f 6d 6d | the Ras|Mol.comm|
|00005210| 61 6e 64 20 6c 69 6e 65 | 2e 0a 0a 20 54 68 65 20 |and line|... The |
|00005220| 56 69 65 77 20 73 75 62 | 2d 6d 65 6e 75 20 61 6e |View sub|-menu an|
|00005230| 64 20 74 68 65 20 22 44 | 6f 74 20 73 75 72 66 61 |d the "D|ot surfa|
|00005240| 63 65 22 20 6f 70 74 69 | 6f 6e 0a 20 2d 2d 2d 2d |ce" opti|on. ----|
|00005250| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00005260| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00005270| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 0a 20 20 54 68 65 |--------|--. The|
|00005280| 73 65 20 61 72 65 20 6d | 69 6e 6f 72 20 6f 70 74 |se are m|inor opt|
|00005290| 69 6f 6e 73 20 6c 69 6b | 65 20 77 68 65 74 68 65 |ions lik|e whethe|
|000052a0| 72 20 6f 72 20 6e 6f 74 | 20 61 78 65 73 20 61 72 |r or not| axes ar|
|000052b0| 65 20 74 6f 20 62 65 20 | 64 69 73 70 6c 61 79 65 |e to be |displaye|
|000052c0| 64 2e 20 54 68 65 20 6f | 6e 6c 79 0a 72 65 61 6c |d. The o|nly.real|
|000052d0| 6c 79 20 69 6d 70 6f 72 | 74 61 6e 74 20 69 74 65 |ly impor|tant ite|
|000052e0| 6d 20 69 73 20 22 44 6f | 74 20 73 75 72 66 61 63 |m is "Do|t surfac|
|000052f0| 65 22 20 77 68 69 63 68 | 20 64 69 73 70 6c 61 79 |e" which| display|
|00005300| 73 20 61 20 56 61 6e 20 | 64 65 72 20 57 61 61 6c |s a Van |der Waal|
|00005310| 27 73 20 64 6f 74 20 73 | 75 72 66 61 63 65 0a 61 |'s dot s|urface.a|
|00005320| 72 6f 75 6e 64 20 65 61 | 63 68 20 61 74 6f 6d 2e |round ea|ch atom.|
|00005330| 20 54 68 65 20 64 65 6e | 73 69 74 79 20 6d 61 79 | The den|sity may|
|00005340| 20 62 65 20 73 70 65 63 | 69 66 69 65 64 20 69 6e | be spec|ified in|
|00005350| 20 74 68 65 20 73 75 62 | 2d 6d 65 6e 75 2c 20 31 | the sub|-menu, 1|
|00005360| 30 30 20 69 73 20 74 68 | 65 20 64 65 66 61 75 6c |00 is th|e defaul|
|00005370| 74 0a 76 61 6c 75 65 2c | 20 62 75 74 20 79 6f 75 |t.value,| but you|
|00005380| 20 63 61 6e 20 65 6e 74 | 65 72 20 76 61 6c 75 65 | can ent|er value|
|00005390| 73 20 75 70 20 74 6f 20 | 31 30 30 30 2e 20 4e 6f |s up to |1000. No|
|000053a0| 74 65 20 74 68 61 74 20 | 74 68 65 20 64 6f 74 20 |te that |the dot |
|000053b0| 73 75 72 66 61 63 65 20 | 69 73 20 61 63 74 75 61 |surface |is actua|
|000053c0| 6c 6c 79 0a 63 61 6c 63 | 75 6c 61 74 65 64 20 61 |lly.calc|ulated a|
|000053d0| 6e 64 20 73 74 6f 72 65 | 64 20 69 6e 20 6d 65 6d |nd store|d in mem|
|000053e0| 6f 72 79 2c 20 73 6f 20 | 74 68 69 73 20 6f 70 74 |ory, so |this opt|
|000053f0| 69 6f 6e 20 74 61 6b 65 | 73 20 73 6f 6d 65 20 63 |ion take|s some c|
|00005400| 6f 6d 70 75 74 61 74 69 | 6f 6e 20 74 69 6d 65 20 |omputati|on time |
|00005410| 61 6e 64 0a 61 6c 73 6f | 20 71 75 69 74 65 20 61 |and.also| quite a|
|00005420| 20 62 69 74 20 6f 66 20 | 6d 65 6d 6f 72 79 20 69 | bit of |memory i|
|00005430| 66 20 74 68 65 20 6d 6f | 6c 65 63 75 6c 65 20 69 |f the mo|lecule i|
|00005440| 73 20 6c 61 72 67 65 2e | 20 55 73 69 6e 67 20 74 |s large.| Using t|
|00005450| 68 65 20 22 63 6f 6c 6f | 75 72 20 64 6f 74 73 22 |he "colo|ur dots"|
|00005460| 20 63 6f 6d 6d 61 6e 64 | 0a 79 6f 75 20 63 61 6e | command|.you can|
|00005470| 20 63 72 65 61 74 65 20 | 73 6f 6d 65 20 69 6e 74 | create |some int|
|00005480| 65 72 65 73 74 69 6e 67 | 20 65 66 66 65 63 74 73 |eresting| effects|
|00005490| 2c 20 65 2e 67 2e 20 22 | 63 6f 6c 6f 75 72 20 64 |, e.g. "|colour d|
|000054a0| 6f 74 73 20 70 6f 74 65 | 6e 74 69 61 6c 22 20 77 |ots pote|ntial" w|
|000054b0| 68 69 63 68 20 63 6f 6c | 6f 75 72 73 0a 74 68 65 |hich col|ours.the|
|000054c0| 20 64 6f 74 73 20 61 63 | 63 6f 72 64 69 6e 67 20 | dots ac|cording |
|000054d0| 74 6f 20 74 68 65 69 72 | 20 65 6c 65 63 74 72 6f |to their| electro|
|000054e0| 73 74 61 74 69 63 20 70 | 6f 74 65 6e 74 69 61 6c |static p|otential|
|000054f0| 2e 0a 0a 20 43 6f 6c 6f | 75 72 73 0a 20 2d 2d 2d |... Colo|urs. ---|
|00005500| 2d 2d 2d 2d 0a 20 20 54 | 68 69 73 20 73 75 62 6d |----. T|his subm|
|00005510| 65 6e 75 20 69 6d 70 6c | 65 6d 65 6e 74 73 20 74 |enu impl|ements t|
|00005520| 68 65 20 52 61 73 4d 6f | 6c 20 22 63 6f 6c 6f 75 |he RasMo|l "colou|
|00005530| 72 22 20 63 6f 6d 6d 61 | 6e 64 2e 20 46 6f 72 20 |r" comma|nd. For |
|00005540| 57 69 72 65 66 72 61 6d | 65 2c 20 53 74 69 63 6b |Wirefram|e, Stick|
|00005550| 73 2c 0a 53 70 61 63 65 | 66 69 6c 6c 20 61 6e 64 |s,.Space|fill and|
|00005560| 20 42 61 6c 6c 26 53 74 | 69 63 6b 20 6d 6f 64 65 | Ball&St|ick mode|
|00005570| 2c 20 79 6f 75 20 77 6f | 75 6c 64 20 6e 6f 72 6d |, you wo|uld norm|
|00005580| 61 6c 6c 79 20 75 73 65 | 20 74 68 65 20 43 50 4b |ally use| the CPK|
|00005590| 20 63 6f 6c 6f 75 72 69 | 6e 67 20 77 68 69 63 68 | colouri|ng which|
|000055a0| 0a 69 73 20 63 68 6f 73 | 65 6e 20 62 79 20 64 65 |.is chos|en by de|
|000055b0| 66 61 75 6c 74 20 77 68 | 65 6e 20 61 20 6d 6f 6c |fault wh|en a mol|
|000055c0| 65 63 75 6c 65 20 69 73 | 20 6c 6f 61 64 65 64 2e |ecule is| loaded.|
|000055d0| 20 43 68 6f 6f 73 69 6e | 67 20 61 20 6d 65 6e 75 | Choosin|g a menu|
|000055e0| 20 69 74 65 6d 20 61 6c | 77 61 79 73 0a 73 65 74 | item al|ways.set|
|000055f0| 73 20 74 68 65 20 63 6f | 6c 6f 75 72 20 73 63 68 |s the co|lour sch|
|00005600| 65 6d 65 20 66 6f 72 20 | 74 68 65 20 77 68 6f 6c |eme for |the whol|
|00005610| 65 20 6f 66 20 74 68 65 | 20 6d 6f 6c 65 63 75 6c |e of the| molecul|
|00005620| 65 2e 0a 20 20 49 66 20 | 79 6f 75 20 77 61 6e 74 |e.. If |you want|
|00005630| 20 74 6f 20 63 6f 6c 6f | 75 72 0a 70 61 72 74 20 | to colo|ur.part |
|00005640| 6f 66 20 61 20 6d 6f 6c | 65 63 75 6c 65 20 75 73 |of a mol|ecule us|
|00005650| 65 20 74 68 65 20 22 73 | 65 6c 65 63 74 22 20 61 |e the "s|elect" a|
|00005660| 6e 64 20 22 63 6f 6c 6f | 75 72 22 20 63 6f 6d 6d |nd "colo|ur" comm|
|00005670| 61 6e 64 73 20 66 72 6f | 6d 20 74 68 65 20 63 6f |ands fro|m the co|
|00005680| 6d 6d 61 6e 64 0a 6c 69 | 6e 65 2e 0a 20 20 46 6f |mmand.li|ne.. Fo|
|00005690| 72 20 64 65 74 61 69 6c | 73 20 6f 6e 20 74 68 65 |r detail|s on the|
|000056a0| 20 63 6f 6c 6f 75 72 20 | 73 63 68 65 6d 65 73 20 | colour |schemes |
|000056b0| 6c 69 73 74 65 64 20 6f | 6e 20 74 68 65 20 6d 65 |listed o|n the me|
|000056c0| 6e 75 2c 20 74 79 70 65 | 20 22 68 65 6c 70 20 3c |nu, type| "help <|
|000056d0| 63 6f 6c 6f 75 72 0a 73 | 63 68 65 6d 65 3e 22 2e |colour.s|cheme>".|
|000056e0| 20 4e 6f 74 65 20 74 68 | 61 74 20 63 68 6f 6f 73 | Note th|at choos|
|000056f0| 69 6e 67 20 22 55 73 65 | 72 22 20 6f 6e 6c 79 20 |ing "Use|r" only |
|00005700| 6d 61 6b 65 73 20 73 65 | 6e 73 65 20 69 66 20 74 |makes se|nse if t|
|00005710| 68 65 20 63 75 72 72 65 | 6e 74 6c 79 20 6c 6f 61 |he curre|ntly loa|
|00005720| 64 65 64 0a 66 69 6c 65 | 20 69 73 20 61 20 50 44 |ded.file| is a PD|
|00005730| 42 20 66 69 6c 65 20 77 | 68 69 63 68 20 63 6f 6e |B file w|hich con|
|00005740| 74 61 69 6e 73 20 75 73 | 65 72 2d 64 65 66 69 6e |tains us|er-defin|
|00005750| 65 64 20 63 6f 6c 6f 75 | 72 20 69 6e 66 6f 72 6d |ed colou|r inform|
|00005760| 61 74 69 6f 6e 2e 0a 0a | 20 54 68 65 20 52 61 73 |ation...| The Ras|
|00005770| 4d 6f 6c 20 43 6f 6d 6d | 61 6e 64 20 4c 69 6e 65 |Mol Comm|and Line|
|00005780| 0a 20 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |. ------|--------|
|00005790| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 0a 20 20 54 68 65 20 |--------|-. The |
|000057a0| 43 6f 6d 6d 61 6e 64 20 | 4c 69 6e 65 20 77 69 6e |Command |Line win|
|000057b0| 64 6f 77 20 61 6c 6c 6f | 77 73 20 79 6f 75 20 74 |dow allo|ws you t|
|000057c0| 6f 20 65 6e 74 65 72 20 | 52 61 73 4d 6f 6c 20 63 |o enter |RasMol c|
|000057d0| 6f 6d 6d 61 6e 64 73 2e | 20 54 68 65 73 65 20 61 |ommands.| These a|
|000057e0| 72 65 20 64 65 73 63 72 | 69 62 65 64 0a 69 6e 20 |re descr|ibed.in |
|000057f0| 74 68 65 20 6d 61 69 6e | 20 52 61 73 4d 6f 6c 20 |the main| RasMol |
|00005800| 6d 61 6e 75 61 6c 2e 20 | 54 79 70 69 63 61 6c 6c |manual. |Typicall|
|00005810| 79 2c 20 74 68 65 20 6d | 65 6e 75 20 65 6e 74 72 |y, the m|enu entr|
|00005820| 69 65 73 20 6f 6e 6c 79 | 20 67 69 76 65 20 61 20 |ies only| give a |
|00005830| 71 75 69 63 6b 65 72 20 | 77 61 79 20 6f 66 0a 61 |quicker |way of.a|
|00005840| 63 63 65 73 73 69 6e 67 | 20 74 68 65 20 6d 6f 73 |ccessing| the mos|
|00005850| 74 20 66 72 65 71 75 65 | 6e 74 6c 79 20 6e 65 65 |t freque|ntly nee|
|00005860| 64 65 64 20 63 6f 6d 6d | 61 6e 64 20 6c 69 6e 65 |ded comm|and line|
|00005870| 20 66 65 61 74 75 72 65 | 73 2e 20 54 68 65 72 65 | feature|s. There|
|00005880| 66 6f 72 65 20 6d 6f 73 | 74 20 6f 66 20 74 68 65 |fore mos|t of the|
|00005890| 0a 6d 65 6e 75 20 6f 70 | 74 69 6f 6e 73 20 61 72 |.menu op|tions ar|
|000058a0| 65 20 6f 6e 6c 79 20 64 | 65 73 63 72 69 62 65 64 |e only d|escribed|
|000058b0| 20 62 72 69 65 66 6c 79 | 20 69 6e 20 74 68 69 73 | briefly| in this|
|000058c0| 20 52 49 53 43 20 4f 53 | 2d 73 70 65 63 69 66 69 | RISC OS|-specifi|
|000058d0| 63 20 66 69 6c 65 2e 20 | 46 6f 72 20 66 75 72 74 |c file. |For furt|
|000058e0| 68 65 72 0a 69 6e 66 6f | 72 6d 61 74 69 6f 6e 2c |her.info|rmation,|
|000058f0| 20 75 73 65 20 52 61 73 | 4d 6f 6c 27 73 20 63 6f | use Ras|Mol's co|
|00005900| 6d 6d 61 6e 64 20 6c 69 | 6e 65 20 68 65 6c 70 20 |mmand li|ne help |
|00005910| 73 79 73 74 65 6d 2e 20 | 45 6e 74 65 72 69 6e 67 |system. |Entering|
|00005920| 20 22 68 65 6c 70 22 20 | 64 69 73 70 6c 61 79 73 | "help" |displays|
|00005930| 0a 69 6e 66 6f 72 6d 61 | 74 69 6f 6e 20 61 62 6f |.informa|tion abo|
|00005940| 75 74 20 74 68 65 20 68 | 65 6c 70 20 73 79 73 74 |ut the h|elp syst|
|00005950| 65 6d 2e 0a 20 20 49 74 | 20 69 73 20 77 6f 72 74 |em.. It| is wort|
|00005960| 68 20 6e 6f 74 69 6e 67 | 20 74 68 61 74 20 79 6f |h noting| that yo|
|00005970| 75 20 6e 65 65 64 20 74 | 6f 20 75 73 65 20 74 68 |u need t|o use th|
|00005980| 65 20 63 6f 6d 6d 61 6e | 64 20 6c 69 6e 65 20 74 |e comman|d line t|
|00005990| 6f 20 75 73 65 20 74 68 | 65 20 70 72 6f 67 72 61 |o use th|e progra|
|000059a0| 6d 0a 74 6f 20 69 74 73 | 20 66 75 6c 6c 20 65 78 |m.to its| full ex|
|000059b0| 74 65 6e 74 2e 20 46 6f | 72 20 65 78 61 6d 70 6c |tent. Fo|r exampl|
|000059c0| 65 2c 20 6d 6f 73 74 20 | 6d 65 6e 75 20 6f 70 74 |e, most |menu opt|
|000059d0| 69 6f 6e 73 20 61 70 70 | 6c 79 20 74 6f 20 74 68 |ions app|ly to th|
|000059e0| 65 20 77 68 6f 6c 65 20 | 6d 6f 6c 65 63 75 6c 65 |e whole |molecule|
|000059f0| 2c 0a 65 2e 67 2e 20 74 | 68 65 20 64 69 73 70 6c |,.e.g. t|he displ|
|00005a00| 61 79 20 74 79 70 65 20 | 6f 72 20 63 6f 6c 6f 75 |ay type |or colou|
|00005a10| 72 20 73 65 74 74 69 6e | 67 73 2e 20 55 73 69 6e |r settin|gs. Usin|
|00005a20| 67 20 74 68 65 20 63 6f | 6d 6d 61 6e 64 20 6c 69 |g the co|mmand li|
|00005a30| 6e 65 2c 20 68 6f 77 65 | 76 65 72 2c 20 69 74 20 |ne, howe|ver, it |
|00005a40| 69 73 0a 70 6f 73 73 69 | 62 6c 65 20 74 6f 20 73 |is.possi|ble to s|
|00005a50| 65 6c 65 63 74 20 70 61 | 72 74 73 20 6f 66 20 74 |elect pa|rts of t|
|00005a60| 68 65 20 6d 6f 6c 65 63 | 75 6c 65 20 28 65 2e 67 |he molec|ule (e.g|
|00005a70| 2e 20 61 6c 6c 20 48 79 | 64 72 6f 67 65 6e 20 61 |. all Hy|drogen a|
|00005a80| 74 6f 6d 73 20 6f 72 20 | 6f 6e 6c 79 20 73 70 65 |toms or |only spe|
|00005a90| 63 69 66 69 63 0a 61 6d | 69 6e 6f 20 61 63 69 64 |cific.am|ino acid|
|00005aa0| 73 29 20 61 6e 64 20 61 | 70 70 6c 79 20 64 69 73 |s) and a|pply dis|
|00005ab0| 70 6c 61 79 20 73 74 79 | 6c 65 20 6f 72 20 63 6f |play sty|le or co|
|00005ac0| 6c 6f 75 72 69 6e 67 20 | 63 6f 6d 6d 61 6e 64 73 |louring |commands|
|00005ad0| 20 74 6f 20 74 68 65 6d | 2e 20 49 6e 20 66 61 63 | to them|. In fac|
|00005ae0| 74 2c 20 6d 6f 73 74 0a | 52 61 73 4d 6f 6c 20 63 |t, most.|RasMol c|
|00005af0| 6f 6d 6d 61 6e 64 73 20 | 6f 6e 6c 79 20 61 66 66 |ommands |only aff|
|00005b00| 65 63 74 20 74 68 65 20 | 63 75 72 72 65 6e 74 20 |ect the |current |
|00005b10| 73 65 6c 65 63 74 69 6f | 6e 20 28 74 79 70 65 20 |selectio|n (type |
|00005b20| 22 68 65 6c 70 20 73 65 | 6c 65 63 74 22 20 74 6f |"help se|lect" to|
|00005b30| 20 66 69 6e 64 20 6f 75 | 74 0a 68 6f 77 20 74 6f | find ou|t.how to|
|00005b40| 20 73 65 6c 65 63 74 20 | 67 72 6f 75 70 73 20 6f | select |groups o|
|00005b50| 66 20 61 74 6f 6d 73 29 | 2e 20 4d 61 6e 79 20 63 |f atoms)|. Many c|
|00005b60| 6f 6d 6d 61 6e 64 73 20 | 74 61 6b 65 20 70 61 72 |ommands |take par|
|00005b70| 61 6d 65 74 65 72 73 20 | 77 68 69 63 68 20 6d 61 |ameters |which ma|
|00005b80| 6b 65 20 74 68 65 6d 20 | 6d 6f 72 65 0a 76 65 72 |ke them |more.ver|
|00005b90| 73 61 74 69 6c 65 20 74 | 68 61 6e 20 74 68 65 69 |satile t|han thei|
|00005ba0| 72 20 6d 65 6e 75 20 63 | 6f 6e 74 65 72 70 61 72 |r menu c|onterpar|
|00005bb0| 74 73 2e 0a 20 20 4f 74 | 68 65 72 20 66 65 61 74 |ts.. Ot|her feat|
|00005bc0| 75 72 65 73 20 69 6e 63 | 6c 75 64 65 20 63 61 6c |ures inc|lude cal|
|00005bd0| 63 75 6c 61 74 69 6f 6e | 20 61 6e 64 20 64 69 73 |culation| and dis|
|00005be0| 70 6c 61 79 20 6f 66 20 | 68 79 64 72 6f 67 65 6e |play of |hydrogen|
|00005bf0| 20 62 6f 6e 64 73 2c 20 | 53 53 2d 62 6f 6e 64 73 | bonds, |SS-bonds|
|00005c00| 2c 0a 63 61 6c 63 75 6c | 61 74 69 6e 67 20 63 6f |,.calcul|ating co|
|00005c10| 6e 6e 65 63 74 69 76 69 | 74 79 20 69 6e 66 6f 72 |nnectivi|ty infor|
|00005c20| 6d 61 74 69 6f 6e 20 66 | 6f 72 20 6d 6f 6c 65 63 |mation f|or molec|
|00005c30| 75 6c 65 20 66 69 6c 65 | 73 20 77 69 74 68 6f 75 |ule file|s withou|
|00005c40| 74 20 62 6f 6e 64 69 6e | 67 20 65 74 63 2e 0a 20 |t bondin|g etc.. |
|00005c50| 20 4e 6f 74 65 20 74 68 | 61 74 20 74 68 65 20 72 | Note th|at the r|
|00005c60| 65 6c 65 61 73 65 20 6e | 6f 74 65 73 20 27 32 36 |elease n|otes '26|
|00005c70| 62 65 74 61 31 27 20 61 | 6e 64 20 27 32 36 62 65 |beta1' a|nd '26be|
|00005c80| 74 61 32 27 20 69 6e 20 | 74 68 65 20 27 44 6f 63 |ta2' in |the 'Doc|
|00005c90| 73 27 20 64 69 72 65 63 | 74 6f 72 79 20 0a 64 65 |s' direc|tory .de|
|00005ca0| 73 63 72 69 62 65 20 61 | 64 64 69 74 69 6f 6e 61 |scribe a|dditiona|
|00005cb0| 6c 20 63 6f 6d 6d 61 6e | 64 73 20 61 6e 64 20 6f |l comman|ds and o|
|00005cc0| 70 74 69 6f 6e 73 20 6e | 6f 74 20 69 6e 63 6c 75 |ptions n|ot inclu|
|00005cd0| 64 65 64 20 69 6e 20 74 | 68 65 20 68 65 6c 70 20 |ded in t|he help |
|00005ce0| 66 69 6c 65 2e 0a 20 20 | 53 6f 6d 65 20 63 6f 6d |file.. |Some com|
|00005cf0| 6d 61 6e 64 20 6c 69 6e | 65 20 63 6f 6d 6d 61 6e |mand lin|e comman|
|00005d00| 64 73 20 69 6e 74 65 72 | 61 63 74 20 77 69 74 68 |ds inter|act with|
|00005d10| 20 74 68 65 20 75 73 65 | 72 20 69 6e 74 65 72 66 | the use|r interf|
|00005d20| 61 63 65 2c 20 65 2e 67 | 2e 20 74 68 65 20 22 53 |ace, e.g|. the "S|
|00005d30| 65 74 20 70 69 63 6b 69 | 6e 67 0a 78 78 78 22 20 |et picki|ng.xxx" |
|00005d40| 63 6f 6d 6d 61 6e 64 73 | 20 77 68 69 63 68 20 64 |commands| which d|
|00005d50| 65 66 69 6e 65 20 77 68 | 61 74 20 68 61 70 70 65 |efine wh|at happe|
|00005d60| 6e 73 20 69 66 20 79 6f | 75 20 63 6c 69 63 6b 20 |ns if yo|u click |
|00005d70| 6f 6e 20 61 6e 20 61 74 | 6f 6d 20 28 73 65 65 20 |on an at|om (see |
|00005d80| 27 32 36 62 65 74 61 31 | 27 29 2e 0a 59 6f 75 20 |'26beta1|')..You |
|00005d90| 63 61 6e 20 6c 61 62 65 | 6c 20 61 74 6f 6d 73 20 |can labe|l atoms |
|00005da0| 61 6e 64 20 66 69 6e 64 | 20 6f 75 74 20 61 62 6f |and find| out abo|
|00005db0| 75 74 20 64 69 73 74 61 | 6e 63 65 73 2c 20 61 6e |ut dista|nces, an|
|00005dc0| 67 6c 65 73 20 61 6e 64 | 20 74 6f 72 73 69 6f 6e |gles and| torsion|
|00005dd0| 73 20 65 74 63 2e 0a 0a | 20 41 64 64 69 74 69 6f |s etc...| Additio|
|00005de0| 6e 61 6c 20 66 69 6c 65 | 20 74 79 70 65 73 0a 20 |nal file| types. |
|00005df0| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00005e00| 2d 2d 2d 2d 2d 0a 20 20 | 46 69 6c 65 73 20 6f 66 |-----. |Files of|
|00005e10| 20 74 68 65 20 66 6f 6c | 6c 6f 77 69 6e 67 20 74 | the fol|lowing t|
|00005e20| 79 70 65 73 20 63 61 6e | 20 6f 6e 6c 79 20 62 65 |ypes can| only be|
|00005e30| 20 6c 6f 61 64 65 64 20 | 75 73 69 6e 67 20 74 68 | loaded |using th|
|00005e40| 65 20 63 6f 6d 6d 61 6e | 64 20 6c 69 6e 65 3a 0a |e comman|d line:.|
|00005e50| 54 72 69 70 6f 73 27 20 | 53 79 62 79 6c 20 4d 6f |Tripos' |Sybyl Mo|
|00005e60| 6c 32 20 66 69 6c 65 20 | 66 6f 72 6d 61 74 2c 20 |l2 file |format, |
|00005e70| 74 68 65 20 43 48 41 52 | 4d 6d 20 66 69 6c 65 20 |the CHAR|Mm file |
|00005e80| 66 6f 72 6d 61 74 20 61 | 6e 64 20 20 4d 53 43 27 |format a|nd MSC'|
|00005e90| 73 20 58 4d 6f 6c 20 58 | 59 5a 0a 66 69 6c 65 20 |s XMol X|YZ.file |
|00005ea0| 66 6f 72 6d 61 74 2e 20 | 54 6f 20 6c 6f 61 64 20 |format. |To load |
|00005eb0| 74 68 65 73 65 2c 20 74 | 79 70 65 20 22 6c 6f 61 |these, t|ype "loa|
|00005ec0| 64 20 3c 66 6f 72 6d 61 | 74 3e 20 3c 66 69 6c 65 |d <forma|t> <file|
|00005ed0| 6e 61 6d 65 3e 22 20 28 | 77 68 65 72 65 20 3c 66 |name>" (|where <f|
|00005ee0| 6f 72 6d 61 74 3e 0a 69 | 73 20 22 6d 6f 6c 32 22 |ormat>.i|s "mol2"|
|00005ef0| 2c 20 22 63 68 61 72 6d | 6d 22 20 6f 72 20 22 78 |, "charm|m" or "x|
|00005f00| 79 7a 22 20 72 65 73 70 | 65 63 74 69 76 65 6c 79 |yz" resp|ectively|
|00005f10| 29 20 61 6e 64 20 70 72 | 65 73 73 20 52 65 74 75 |) and pr|ess Retu|
|00005f20| 72 6e 2e 20 41 6c 74 65 | 72 6e 61 74 69 76 65 6c |rn. Alte|rnativel|
|00005f30| 79 2c 0a 74 79 70 65 20 | 22 6c 6f 61 64 20 3c 66 |y,.type |"load <f|
|00005f40| 6f 72 6d 61 74 3e 20 22 | 20 61 6e 64 20 64 72 61 |ormat> "| and dra|
|00005f50| 67 20 74 68 65 20 66 69 | 6c 65 20 74 6f 20 74 68 |g the fi|le to th|
|00005f60| 65 20 43 6f 6d 6d 61 6e | 64 20 4c 69 6e 65 20 77 |e Comman|d Line w|
|00005f70| 69 6e 64 6f 77 2e 20 54 | 68 65 6e 0a 70 72 65 73 |indow. T|hen.pres|
|00005f80| 73 20 74 68 65 20 52 65 | 74 75 72 6e 20 6b 65 79 |s the Re|turn key|
|00005f90| 2e 0a 0a 20 20 4e 6f 74 | 65 20 74 68 61 74 20 79 |... Not|e that y|
|00005fa0| 6f 75 20 63 61 6e 20 6f | 6e 6c 79 20 68 61 76 65 |ou can o|nly have|
|00005fb0| 20 6f 6e 65 20 66 69 6c | 65 20 6c 6f 61 64 65 64 | one fil|e loaded|
|00005fc0| 20 61 74 20 61 20 74 69 | 6d 65 2e 20 49 66 20 79 | at a ti|me. If y|
|00005fd0| 6f 75 20 74 72 79 20 74 | 6f 20 6c 6f 61 64 0a 61 |ou try t|o load.a|
|00005fe0| 20 66 69 6c 65 20 66 72 | 6f 6d 20 74 68 65 20 63 | file fr|om the c|
|00005ff0| 6f 6d 6d 61 6e 64 20 6c | 69 6e 65 20 77 68 69 6c |ommand l|ine whil|
|00006000| 65 20 74 68 65 72 65 20 | 69 73 20 61 20 66 69 6c |e there |is a fil|
|00006010| 65 20 69 6e 20 6d 65 6d | 6f 72 79 2c 20 79 6f 75 |e in mem|ory, you|
|00006020| 20 67 65 74 20 61 6e 0a | 65 72 72 6f 72 20 6d 65 | get an.|error me|
|00006030| 73 73 61 67 65 2e 20 49 | 66 20 74 68 69 73 20 68 |ssage. I|f this h|
|00006040| 61 70 70 65 6e 73 2c 20 | 63 6c 65 61 72 20 74 68 |appens, |clear th|
|00006050| 65 20 64 61 74 61 62 61 | 73 65 20 62 79 20 65 6e |e databa|se by en|
|00006060| 74 65 72 69 6e 67 20 22 | 7a 61 70 22 2c 20 74 68 |tering "|zap", th|
|00006070| 65 6e 0a 74 72 79 20 61 | 67 61 69 6e 2e 20 49 66 |en.try a|gain. If|
|00006080| 20 79 6f 75 20 6c 6f 61 | 64 20 61 20 66 69 6c 65 | you loa|d a file|
|00006090| 20 62 79 20 64 72 61 67 | 67 69 6e 67 20 69 74 20 | by drag|ging it |
|000060a0| 74 6f 20 74 68 65 20 70 | 72 6f 67 72 61 6d 20 6f |to the p|rogram o|
|000060b0| 72 20 62 79 20 64 6f 75 | 62 6c 65 2d 0a 63 6c 69 |r by dou|ble-.cli|
|000060c0| 63 6b 69 6e 67 20 6f 6e | 20 69 74 2c 20 74 68 65 |cking on| it, the|
|000060d0| 20 64 61 74 61 62 61 73 | 65 20 69 73 20 63 6c 65 | databas|e is cle|
|000060e0| 61 72 65 64 20 61 75 74 | 6f 6d 61 74 69 63 61 6c |ared aut|omatical|
|000060f0| 6c 79 20 62 65 66 6f 72 | 65 20 74 68 65 20 66 69 |ly befor|e the fi|
|00006100| 6c 65 20 69 73 0a 6c 6f | 61 64 65 64 2e 0a 0a 20 |le is.lo|aded... |
|00006110| 4c 69 6e 6b 73 20 74 6f | 20 6d 6f 6c 65 63 75 6c |Links to| molecul|
|00006120| 65 20 64 61 74 61 62 61 | 6e 6b 73 20 61 6e 64 20 |e databa|nks and |
|00006130| 57 57 57 20 70 61 67 65 | 73 20 61 62 6f 75 74 20 |WWW page|s about |
|00006140| 52 61 73 4d 6f 6c 0a 20 | 2d 2d 2d 2d 2d 2d 2d 2d |RasMol. |--------|
|00006150| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00006160| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 2d 2d |--------|--------|
|00006170| 2d 2d 2d 2d 2d 2d 2d 2d | 2d 2d 2d 2d 2d 2d 0a 54 |--------|------.T|
|00006180| 68 65 20 52 61 73 4d 6f | 6c 20 57 57 57 20 68 6f |he RasMo|l WWW ho|
|00006190| 6d 65 20 70 61 67 65 3a | 20 20 20 20 68 74 74 70 |me page:| http|
|000061a0| 3a 2f 2f 6b 6c 61 61 74 | 75 2e 6f 69 74 2e 75 6d |://klaat|u.oit.um|
|000061b0| 61 73 73 2e 65 64 75 3a | 38 30 2f 6d 69 63 72 6f |ass.edu:|80/micro|
|000061c0| 62 69 6f 2f 72 61 73 6d | 6f 6c 2f 0a 54 68 69 73 |bio/rasm|ol/.This|
|000061d0| 20 70 61 67 65 20 69 73 | 20 70 72 6f 76 69 64 65 | page is| provide|
|000061e0| 64 20 62 79 20 45 72 69 | 63 20 4d 61 72 74 7a 2e |d by Eri|c Martz.|
|000061f0| 20 49 74 20 63 6f 6e 74 | 61 69 6e 73 20 66 72 65 | It cont|ains fre|
|00006200| 71 75 65 6e 74 6c 79 20 | 75 70 64 61 74 65 64 20 |quently |updated |
|00006210| 69 6e 66 6f 72 6d 61 74 | 69 6f 6e 0a 61 62 6f 75 |informat|ion.abou|
|00006220| 74 20 52 61 73 4d 6f 6c | 20 61 6e 64 20 6c 6f 74 |t RasMol| and lot|
|00006230| 73 20 6f 66 20 6c 69 6e | 6b 73 20 74 6f 20 73 69 |s of lin|ks to si|
|00006240| 74 65 73 20 77 68 65 72 | 65 20 79 6f 75 20 63 61 |tes wher|e you ca|
|00006250| 6e 20 67 65 74 20 6d 6f | 6c 65 63 75 6c 65 20 66 |n get mo|lecule f|
|00006260| 69 6c 65 73 2e 0a 0a 41 | 6e 20 65 6e 6f 72 6d 6f |iles...A|n enormo|
|00006270| 75 73 20 63 6f 6c 6c 65 | 63 74 69 6f 6e 20 6f 66 |us colle|ction of|
|00006280| 20 70 72 6f 74 65 69 6e | 73 20 69 73 20 61 76 61 | protein|s is ava|
|00006290| 69 6c 61 62 6c 65 20 66 | 72 6f 6d 20 74 68 65 20 |ilable f|rom the |
|000062a0| 42 72 6f 6f 6b 68 61 76 | 65 6e 20 50 72 6f 74 65 |Brookhav|en Prote|
|000062b0| 69 6e 0a 44 61 74 61 62 | 61 6e 6b 20 61 74 20 77 |in.Datab|ank at w|
|000062c0| 77 77 2e 70 64 62 2e 62 | 6e 6c 2e 67 6f 76 2e 0a |ww.pdb.b|nl.gov..|
|000062d0| 0a 4f 6b 61 6e 61 67 61 | 6e 20 55 6e 69 76 65 72 |.Okanaga|n Univer|
|000062e0| 73 69 74 79 20 6d 6f 6c | 65 63 75 6c 65 20 66 69 |sity mol|ecule fi|
|000062f0| 6c 65 73 3a 20 68 74 74 | 70 3a 2f 2f 77 77 77 2e |les: htt|p://www.|
|00006300| 6f 6b 61 6e 61 67 61 6e | 2e 62 63 2e 63 61 2f 63 |okanagan|.bc.ca/c|
|00006310| 68 65 6d 2f 6d 6f 6c 65 | 63 75 6c 65 2f 0a 0a 41 |hem/mole|cule/..A|
|00006320| 6e 64 20 6d 61 6e 79 20 | 6d 6f 72 65 20 77 68 69 |nd many |more whi|
|00006330| 63 68 20 79 6f 75 20 77 | 69 6c 6c 20 66 69 6e 64 |ch you w|ill find|
|00006340| 20 6f 6e 20 74 68 65 20 | 52 61 73 4d 6f 6c 20 57 | on the |RasMol W|
|00006350| 57 57 20 68 6f 6d 65 20 | 70 61 67 65 2e 0a 0a 20 |WW home |page... |
|00006360| 48 69 73 74 6f 72 79 0a | 20 2d 2d 2d 2d 2d 2d 2d |History.| -------|
|00006370| 0a 20 56 65 72 73 69 6f | 6e 20 31 2e 32 30 20 28 |. Versio|n 1.20 (|
|00006380| 31 39 2d 30 38 2d 39 36 | 29 3a 0a 20 2d 20 62 61 |19-08-96|):. - ba|
|00006390| 73 65 64 20 6f 6e 20 52 | 61 73 4d 6f 6c 20 32 2e |sed on R|asMol 2.|
|000063a0| 36 62 65 74 61 32 0a 20 | 2d 20 75 70 64 61 74 65 |6beta2. |- update|
|000063b0| 64 20 74 68 69 73 20 21 | 48 65 6c 70 20 66 69 6c |d this !|Help fil|
|000063c0| 65 0a 20 2d 20 69 6e 63 | 6c 75 64 65 64 20 32 36 |e. - inc|luded 26|
|000063d0| 62 65 74 61 31 20 61 6e | 64 20 32 36 62 65 74 61 |beta1 an|d 26beta|
|000063e0| 32 20 72 65 6c 65 61 73 | 65 20 6e 6f 74 65 73 0a |2 releas|e notes.|
|000063f0| 20 20 20 28 73 6c 69 67 | 68 6c 79 20 6d 6f 64 69 | (slig|hly modi|
+--------+-------------------------+-------------------------+--------+--------+
Only 25.0 KB of data is shown above.