From: Esben J. B. <esb...@ro...> - 2013-04-18 08:59:19
|
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 |
From: Jason V. <jas...@sc...> - 2013-04-19 17:06:23
|
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 <esb...@ro...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Esben J. B. <esb...@ro...> - 2013-04-22 11:15:56
|
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 <jas...@sc...> To: Esben Jannik Bjerrum <Esb...@ro...> Cc: "pym...@li..." <pym...@li...> 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 <esb...@ro...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Thomas H. <tho...@sc...> - 2013-04-22 12:31:24
|
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 <jas...@sc...> > To: Esben Jannik Bjerrum <Esb...@ro...> > Cc: "pym...@li..." > 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 > <esb...@ro... <mailto:esb...@ro...>> 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 |
From: Gianluigi C. <chi...@ya...> - 2013-04-22 16:49:29
|
Hi all, I often use VASCo surfaces and I am experiencing a strange behaviour on transparency settings as VASCo surfaces do not "respond" to: set transparency, value, object Not from the command line, not from the plugin itself. Pymol's surfaces get transparent but not the object corresponding to VASCo surface. I am not sure but I would say it worked to me before. I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid). Am I missing something? thanks and regards Gianluigi |
From: Thomas H. <tho...@sc...> - 2013-04-24 06:55:27
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Hi Gianluigi, that surface is a CGO object, so you need: set cgo_transparency, value, object Hope that helps. Cheers, Thomas Gianluigi Caltabiano wrote, On 04/22/13 18:49: > Hi all, > > I often use VASCo surfaces and I am experiencing a strange behaviour on > transparency settings as VASCo surfaces do not "respond" to: > set transparency, value, object > Not from the command line, not from the plugin itself. Pymol's surfaces > get transparent but not the object corresponding to VASCo surface. > I am not sure but I would say it worked to me before. > I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid). > > Am I missing something? > > thanks and regards > > Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor |