Angel and Nico 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. >> >>As they say, my other 2 cents... >> >> > 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 ?)
In the general case, the residue sequence numbers in .pdb files are completely unordered. > : if you have 17, 20, 19 would 20 be selected by 17-19 ? Yes. It must be. If it is not selected then insertion codes will never work. > Concerning the behaviour with 19-17, I would say it is the same as 17-19. > It may be easier to write scripts OK A residue sequence number is only an identifier for that particular residue. It may have a character insertion code. 1 2a 3 99z -5b 4 In the case identified by Rolf, they are not even unique identifiers. 1 2 3 4 5 1 2 3 4 5 So, given this information ... Q: Are 'select 17-19' and 'select 19-17' the same thing? Nico, you said 'yes' to this. Let's assume that the file looks like this 1 2 3 4 5 4 3 2 1 If someone says 'select 3-5' ... what should be selected? Miguel ------------------------------------------------------- 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
