Hi Esben, It's up to you to decide how you want to handle this. You have a few options.
You can remove unwanted alternate conformations, for example: remove not alt ''+'A' then run your script. Or you can specify PyMOL only add hydrogens to a certain set of conformations: # only h_add to alt conformations labeled 'C' h_add 1zw9 and alt 'C' To only add hydrogens to default or 'A' conformers do the following: h_add 1zw9 and alt ''+'A' Cheers, -- Jason On Thu, Apr 18, 2013 at 3:59 AM, Esben Jannik Bjerrum <esbenjan...@rocketmail.com> wrote: > Hi Pymol Users > I have a problem with wrong atom assignment, and subsequently wrong > addition of hydrogens, if theres alternate conformations present. I hope > anyone else has experience with this or suggestions for troubleshooting. > I have developed some scripts that downloads pdb-files from a list, add > hydrogens to them, and otherwise prepares them for further usage. However, > if theres alternate conformations present, the atoms on the backbone gets a > wrong charge assignemt or something, breaking the subsequent addition of > hydrogens. It seems to happen at PDB load time. > > Example steps to reproduce > fetch 1zw9 > zoom resi 12 > h_add 1zw9 > > the hydrogen on the nitrogen in the backbone peptide bond doesn't make a > planer configuration, and if I save the object, the oxygen is assigned a -1 > charge. This makes troubles in my subsequent workflow. > > I've tried to delete the alternate conformations inside PyMOL before adding > hydrogens, but that doesnt fix the problem. I can fix the problem by > removing the alternate conformations from the PDB file before I load it into > pymol, but I would rather fix it inside pymol in my scripts. > > Best Regards > Esben Jannik Bjerrum > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ 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
