[PyMOL] Adding hydrogens
Dear PyMOL list I'm adding hydrogens to a crystal structure. Upon saving, however, I realize all hydrogens have been added to the beginning of the PDB file. Can PyMOL be configured such that the hydrogens are placed at the intuitively appropriate place in the PDB file? Thanks for any hints. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
Re: [PyMOL] Adding hydrogens
Hi Martin, do you have retain_order set to 1? This is not the default. Try: unset retain_order save file.pdb Cheers, Thomas Martin Hediger wrote, On 09/25/12 18:24: Dear PyMOL list I'm adding hydrogens to a crystal structure. Upon saving, however, I realize all hydrogens have been added to the beginning of the PDB file. Can PyMOL be configured such that the hydrogens are placed at the intuitively appropriate place in the PDB file? Thanks for any hints. Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
Re: [PyMOL] Adding Hydrogens
Dear all, thanks for the feedback, I'll definitely give it a try. On 16.03.11 16:50, Michael Lerner wrote: I've had good results with MolProbity (http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15 http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15) in the past. I had a script that would let me cycle through all of the HIS residues, add hydrogens, and cycle between states. It's broken at the moment. The trick was that PyMOL doesn't care about the name of the residue, so you have to manually cycle the valences. On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger ma@bluewin.ch mailto:ma@bluewin.ch wrote: Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue gets protonated: His can be protonated at Nd, or Ne or both. Is there a way to control this? On a more general note: what other smart hydrogen adding tools are there out there anyway? Does anyone know a really smart tool for this? I know OpenBabel has a pH parameter. But on the other hand OpenBabel just appends the hydrogens to the PDB file, whereas PyMOL really writes them within the block of atoms corresponding to one residue. Also, AutoDock can add hydrogens and it even has an option for the protonation state of histidine, but it doesn't seem to work in my case. Thanks for your answers and input. martin -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net mailto: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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ 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] Adding Hydrogens
Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue gets protonated: His can be protonated at Nd, or Ne or both. Is there a way to control this? On a more general note: what other smart hydrogen adding tools are there out there anyway? Does anyone know a really smart tool for this? I know OpenBabel has a pH parameter. But on the other hand OpenBabel just appends the hydrogens to the PDB file, whereas PyMOL really writes them within the block of atoms corresponding to one residue. Also, AutoDock can add hydrogens and it even has an option for the protonation state of histidine, but it doesn't seem to work in my case. Thanks for your answers and input. martin -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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
Re: [PyMOL] Adding Hydrogens
I've had good results with MolProbity ( http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15) in the past. I had a script that would let me cycle through all of the HIS residues, add hydrogens, and cycle between states. It's broken at the moment. The trick was that PyMOL doesn't care about the name of the residue, so you have to manually cycle the valences. On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger ma@bluewin.ch wrote: Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue gets protonated: His can be protonated at Nd, or Ne or both. Is there a way to control this? On a more general note: what other smart hydrogen adding tools are there out there anyway? Does anyone know a really smart tool for this? I know OpenBabel has a pH parameter. But on the other hand OpenBabel just appends the hydrogens to the PDB file, whereas PyMOL really writes them within the block of atoms corresponding to one residue. Also, AutoDock can add hydrogens and it even has an option for the protonation state of histidine, but it doesn't seem to work in my case. Thanks for your answers and input. martin -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ 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] Adding Hydrogens to GFP Chromophore
Hi all, I'm trying to use PyMol to add hydrogen atoms to this small fragment of a PDB file, the chromophore from the GFP structure 1EMA; REMARK S65T Chromophore from Ormo's coordintes (1EMB). HETATM 466 N1 CRO66 24.077 27.513 36.610 1.00 11.86 N HETATM 467 CA1 CRO66 25.011 26.478 37.078 1.00 7.34 C HETATM 468 CB1 CRO66 25.931 26.035 35.930 1.00 10.77 C HETATM 469 CG1 CRO66 25.155 25.422 34.796 1.00 16.67 C HETATM 470 OG1 CRO66 26.679 27.129 35.461 1.00 14.22 O HETATM 471 C1 CRO66 25.730 27.106 38.245 1.00 18.38 C HETATM 472 N2 CRO66 26.975 27.732 38.216 1.00 9.21 N HETATM 473 N3 CRO66 25.274 27.124 39.509 1.00 17.10 N HETATM 474 C2 CRO66 26.043 27.875 40.370 1.00 5.46 C HETATM 475 O2 CRO66 26.022 27.962 41.566 1.00 13.20 O HETATM 476 CA2 CRO66 27.197 28.245 39.512 1.00 16.08 C HETATM 477 CA3 CRO66 23.919 26.721 39.842 1.00 10.87 C HETATM 478 C3 CRO66 23.745 25.326 40.360 1.00 19.28 C HETATM 479 O3 CRO66 22.885 25.116 41.193 1.00 15.72 O HETATM 480 CB2 CRO66 28.329 28.822 39.960 1.00 10.75 C HETATM 481 CG2 CRO66 29.437 29.370 39.124 1.00 7.67 C HETATM 482 CD1 CRO66 29.541 29.103 37.742 1.00 11.31 C HETATM 483 CD2 CRO66 30.487 30.110 39.805 1.00 10.79 C HETATM 484 CE1 CRO66 30.707 29.546 37.033 1.00 17.44 C HETATM 485 CE2 CRO66 31.614 30.563 39.085 1.00 10.01 C HETATM 486 CZ CRO66 31.718 30.300 37.721 1.00 9.48 C HETATM 487 OH CRO66 32.894 30.804 36.971 1.00 13.84 O CONECT 466 457 467 CONECT 467 466 468 471 CONECT 468 467 469 470 CONECT 469 468 CONECT 470 468 CONECT 471 467 472 473 CONECT 472 471 476 CONECT 473 471 474 477 CONECT 474 473 475 476 CONECT 475 474 CONECT 476 472 474 480 CONECT 477 473 478 CONECT 478 477 479 488 CONECT 479 478 CONECT 480 476 481 CONECT 481 480 482 483 CONECT 482 481 484 CONECT 483 481 485 CONECT 484 482 486 CONECT 485 483 486 CONECT 486 484 485 487 CONECT 487 486 END Unfortunately, PyMol adds too many hydrogens to each carbon in the tyrosine ring in the center of the chromophore. It doesn't recognize that some of the carbons can have double bonds. Does anyone know the best way to get PyMol to recognize the double bonds? All the best, --Buz |-| Buz Barstow 192 Clark Hall Cornell University Ithaca, NY 14853, USA Email: b...@cornell.edu Phone: 607 255 8678 Fax: 607 255 8751 |-|
RE: [PyMOL] Adding Hydrogens to GFP Chromophore
Buz, You must fix the bond valences manually... Mouse menu - 3 button editing mode Ctrl-right click on bond Ctrl-W to cycle valence (repeat as necessary to get correct valences) Then optinally remove hydrogens when done (use the action [A] menu on the object - remove hydrogens) Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Buz Barstow Sent: Wednesday, March 23, 2005 7:54 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Adding Hydrogens to GFP Chromophore Hi all, I'm trying to use PyMol to add hydrogen atoms to this small fragment of a PDB file, the chromophore from the GFP structure 1EMA; REMARK S65T Chromophore from Ormo's coordintes (1EMB). HETATM 466 N1 CRO66 24.077 27.513 36.610 1.00 11.86 N HETATM 467 CA1 CRO66 25.011 26.478 37.078 1.00 7.34 C HETATM 468 CB1 CRO66 25.931 26.035 35.930 1.00 10.77 C HETATM 469 CG1 CRO66 25.155 25.422 34.796 1.00 16.67 C HETATM 470 OG1 CRO66 26.679 27.129 35.461 1.00 14.22 O HETATM 471 C1 CRO66 25.730 27.106 38.245 1.00 18.38 C HETATM 472 N2 CRO66 26.975 27.732 38.216 1.00 9.21 N HETATM 473 N3 CRO66 25.274 27.124 39.509 1.00 17.10 N HETATM 474 C2 CRO66 26.043 27.875 40.370 1.00 5.46 C HETATM 475 O2 CRO66 26.022 27.962 41.566 1.00 13.20 O HETATM 476 CA2 CRO66 27.197 28.245 39.512 1.00 16.08 C HETATM 477 CA3 CRO66 23.919 26.721 39.842 1.00 10.87 C HETATM 478 C3 CRO66 23.745 25.326 40.360 1.00 19.28 C HETATM 479 O3 CRO66 22.885 25.116 41.193 1.00 15.72 O HETATM 480 CB2 CRO66 28.329 28.822 39.960 1.00 10.75 C HETATM 481 CG2 CRO66 29.437 29.370 39.124 1.00 7.67 C HETATM 482 CD1 CRO66 29.541 29.103 37.742 1.00 11.31 C HETATM 483 CD2 CRO66 30.487 30.110 39.805 1.00 10.79 C HETATM 484 CE1 CRO66 30.707 29.546 37.033 1.00 17.44 C HETATM 485 CE2 CRO66 31.614 30.563 39.085 1.00 10.01 C HETATM 486 CZ CRO66 31.718 30.300 37.721 1.00 9.48 C HETATM 487 OH CRO66 32.894 30.804 36.971 1.00 13.84 O CONECT 466 457 467 CONECT 467 466 468 471 CONECT 468 467 469 470 CONECT 469 468 CONECT 470 468 CONECT 471 467 472 473 CONECT 472 471 476 CONECT 473 471 474 477 CONECT 474 473 475 476 CONECT 475 474 CONECT 476 472 474 480 CONECT 477 473 478 CONECT 478 477 479 488 CONECT 479 478 CONECT 480 476 481 CONECT 481 480 482 483 CONECT 482 481 484 CONECT 483 481 485 CONECT 484 482 486 CONECT 485 483 486 CONECT 486 484 485 487 CONECT 487 486 END Unfortunately, PyMol adds too many hydrogens to each carbon in the tyrosine ring in the center of the chromophore. It doesn't recognize that some of the carbons can have double bonds. Does anyone know the best way to get PyMol to recognize the double bonds? All the best, --Buz |-| Buz Barstow 192 Clark Hall Cornell University Ithaca, NY 14853, USA Email: b...@cornell.edu Phone: 607 255 8678 Fax: 607 255 8751 |-| --- This SF.net email is sponsored by Microsoft Mobile Embedded DevCon 2005 Attend MEDC 2005 May 9-12 in Vegas. Learn more about the latest Windows Embedded(r) Windows Mobile(tm) platforms, applications content. Register by 3/29 save $300 http://ads.osdn.com/?ad_id=6883alloc_id=15149op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
