Re: [PyMOL] Dynoplot/Get residues was:[Re: New Feature Ideas]
This is one of the reasons I love open-source: On Thu, Jan 21, 2010 at 7:58 AM, David Hall wrote: > So, I figured it would be nicer if I sent the author a patch instead of just > complaining, so I went to look at the code. To answer your question, iterate and alter scan over the residues in order. (If you make updates to the sequence or IDs in the sequence don't forget to issue the "sort" command.) I ran into this exact problem when I wrote CEalign--missing residues. Using iterate/alter over a selection should solve your problem. Good luck, let me know if I can help you out. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Dynoplot/Get residues was:[Re: New Feature Ideas]
> You would have to work with the DynoPlot author to improve this. So, I figured it would be nicer if I sent the author a patch instead of just complaining, so I went to look at the code. Right now, it uses integer math to try to find the residues before and after, but I know from my mistakes that is generally a bad idea as it ignores insertion codes (eg 82A, 82B in chain H of 1bgx). I think I can get a list of residues in a chain in order by doing iterate. For example: >iterate 1bgx and chain h and name CA, print resi seems to give me the residues in the correct sequence. With the correct syntax, this would give me a list in python. Is this guaranteed to be the correct order? Should we have a get_residues method in addition to get_chains that is guaranteed to produce residues in the correct sequence? -David -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
