On Wednesday, September 07, 2005, at 02:50PM, Nicolas Vervelle <[EMAIL PROTECTED]> wrote:
>Angel Herraez wrote: > >>I don't agree; I understand "17-19" means "17, 18 or 19" --and think any >>casual user would >>see it the same way--; you can know scripts and use them on the console >>without looking at >>the innards of the pdb file. Of course, in this approach "select 19-17" >>doesn't make much >>sense -I doubt anybody would use it-, but what happens if the file is >>unordered (19-18-17), >>the user doesn't know it, and tries to select residues 17 through 19? (s)he >>gets nothing! >>In summary, I see that residue numbers are a way to refer to the residues by >>their identity >>(biochemical meaning), not how they are written in the coordinates file. >> >> >I tend to agree with Angel, select shouldn't depend on the order in the >pdb file. >Otherwise, what would happen with a file completely unordered (is it >possible ?) : if you have 17, 20, 19 would 20 be selected by 17-19 ? > >Concerning the behaviour with 19-17, I would say it is the same as 17-19. >It may be easier to write scripts > I think select 17-19 should work irregardless of the order of residues in the pdb file. select 19-17 should not work anywhere because it doesn't make sense. :-) plus it is too easy (for scripters) to make sure your select command puts the biggest number last. fwiw, the pdb spec does not disallow unordered residues in the list: " In most cases, the amino acids that comprise a protein are numbered sequentially starting with 1. However, there are a number of situations that may give rise to different numbering schemes " and it gives several good reasons why you may see unordered numbering. <http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html> yet another other two cents ;-) tim -- Timothy Driscoll molvisions - See. Grasp. Learn. <http://www.molvisions.com/> earth : usa : virginia : blacksburg ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
