Hi Esben, this works for me:
fetch 1zw9, async=0 remove not alt +A valence guess, 1zw9 h_add 1zw9 Cheers, Thomas Esben Jannik Bjerrum wrote, On 04/22/13 13:15: > Hi Jason and Troels > Thanks for your suggestions, but removing the alternate conformation > doesnt solve the problem in itself. I have already played around with > removing the alternate conformation using the alt selection method, and > the only way successfull is to delete the alternate conformation from > the PDB file, then reload it into Pymol. Pymol doesnt initialise the > backbone bond order or something, when theres an alternate conformation, > and is thus not able to assign the correct hydrogens, even after the > alternate conformation has been deleted. > > Heres an example of an updated script with problems. > fetch 1zw9 > zoom resi 12 > remove not alt ''+'A' > h_add 1zw9 > > Look at the hydrogen at the backbone nitrogen of resi 12 and carbonyl > carbon at resi 11. > > whereas this hackish script works > > fetch 1zw9 > remove not alt ''+'A' > save temp.pdb, 1zw9 > delete 1zw9 > load temp.pdb, 1zw9 > h_add 1zw9 > zoom resi 12 > > Is there a command to get PyMOL to reparse the structure after removing > the alternate conformations? > > Best Regards > Esben Jannik Bjerrum > > > ------------------------------------------------------------------------ > From: Jason Vertrees <jason.vertr...@schrodinger.com> > To: Esben Jannik Bjerrum <esbenjan...@rocketmail.com> > Cc: "pymol-users@lists.sourceforge.net" > Sent: Friday, April 19, 2013 6:43 PM > Subject: Re: [PyMOL] Problems with H_add when theres alternate > conformations present > > 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 <mailto: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 Bjerru -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ 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
