[PyMOL] Interleaved atoms when creating from two objects
I'm working on a script which involves joining two objects together, which I do using the create command. The input objects have different chain identifiers, but identical residue numbers. When I create the joined object, I would expect all atoms from the first object to be added, followed by all atoms from the second object (with atom IDs being unchanged for the first object, and then continuing sequentially for the second object). Instead, the produced object alternates between atoms of each of the input objects: PyMOLiterate joined, print (ID,chain,name) (0, 'A', 'N') (1, 'B', 'N') (2, 'A', 'CA') (3, 'B', 'CA') (4, 'A', 'C') (5, 'B', 'C') (6, 'A', 'O') (7, 'B', 'O') ... This order breaks cartoon and ribbon representations, as well as makes the sequence view display each atom individually rather than combining residues. A somewhat convoluted but reproducible case follows (Using MacPyMOL 1.7.4): fetch 4rp9, type=pdb1 split_states 4rp9 alter 4rp9_0002, chain = 'B' create joined, 4rp9_* and resi 282 I've tried various combinations of the rebuild and sort commands, as well as manually changing the IDs of the objects, but I haven't been able to find a workaround yet. Sort seems to operate on the resi and ignores the ID chain. Is this a bug or am I doing something wrong? Thanks, Spencer -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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] Interleaved atoms when creating from two objects
Hi, I had problems with the retain order setting as well. The autodock vina pulgin turns it on. Unload the plugin to fix it, or manually set it after plugins are loaded. Matt On 4/22/15 8:56 PM, Thomas Holder wrote: Hi Spencer, please check your retain_order setting, it should be off (default). If it's on, also check your pymolrc if you're setting it there. http://www.pymolwiki.org/index.php/Retain_order http://www.pymolwiki.org/index.php/Pymolrc Cheers, Thomas On 22 Apr 2015, at 20:39, Spencer Bliven sbli...@ucsd.edu wrote: I'm working on a script which involves joining two objects together, which I do using the create command. The input objects have different chain identifiers, but identical residue numbers. When I create the joined object, I would expect all atoms from the first object to be added, followed by all atoms from the second object (with atom IDs being unchanged for the first object, and then continuing sequentially for the second object). Instead, the produced object alternates between atoms of each of the input objects: PyMOLiterate joined, print (ID,chain,name) (0, 'A', 'N') (1, 'B', 'N') (2, 'A', 'CA') (3, 'B', 'CA') (4, 'A', 'C') (5, 'B', 'C') (6, 'A', 'O') (7, 'B', 'O') ... This order breaks cartoon and ribbon representations, as well as makes the sequence view display each atom individually rather than combining residues. A somewhat convoluted but reproducible case follows (Using MacPyMOL 1.7.4): fetch 4rp9, type=pdb1 split_states 4rp9 alter 4rp9_0002, chain = 'B' create joined, 4rp9_* and resi 282 I've tried various combinations of the rebuild and sort commands, as well as manually changing the IDs of the objects, but I haven't been able to find a workaround yet. Sort seems to operate on the resi and ignores the ID chain. Is this a bug or am I doing something wrong? Thanks, Spencer -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ 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] Interleaved atoms when creating from two objects
Hi Spencer, please check your retain_order setting, it should be off (default). If it's on, also check your pymolrc if you're setting it there. http://www.pymolwiki.org/index.php/Retain_order http://www.pymolwiki.org/index.php/Pymolrc Cheers, Thomas On 22 Apr 2015, at 20:39, Spencer Bliven sbli...@ucsd.edu wrote: I'm working on a script which involves joining two objects together, which I do using the create command. The input objects have different chain identifiers, but identical residue numbers. When I create the joined object, I would expect all atoms from the first object to be added, followed by all atoms from the second object (with atom IDs being unchanged for the first object, and then continuing sequentially for the second object). Instead, the produced object alternates between atoms of each of the input objects: PyMOLiterate joined, print (ID,chain,name) (0, 'A', 'N') (1, 'B', 'N') (2, 'A', 'CA') (3, 'B', 'CA') (4, 'A', 'C') (5, 'B', 'C') (6, 'A', 'O') (7, 'B', 'O') ... This order breaks cartoon and ribbon representations, as well as makes the sequence view display each atom individually rather than combining residues. A somewhat convoluted but reproducible case follows (Using MacPyMOL 1.7.4): fetch 4rp9, type=pdb1 split_states 4rp9 alter 4rp9_0002, chain = 'B' create joined, 4rp9_* and resi 282 I've tried various combinations of the rebuild and sort commands, as well as manually changing the IDs of the objects, but I haven't been able to find a workaround yet. Sort seems to operate on the resi and ignores the ID chain. Is this a bug or am I doing something wrong? Thanks, Spencer -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ 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] Interleaved atoms when creating from two objects
Thanks, it was indeed due to the autodock plugin setting retain_order. That would have taken me quite a while to debug on my own! -Spencer On Wed, Apr 22, 2015 at 6:03 PM, Matthew Baumgartner mp...@pitt.edu wrote: Hi, I had problems with the retain order setting as well. The autodock vina pulgin turns it on. Unload the plugin to fix it, or manually set it after plugins are loaded. Matt On 4/22/15 8:56 PM, Thomas Holder wrote: Hi Spencer, please check your retain_order setting, it should be off (default). If it's on, also check your pymolrc if you're setting it there. http://www.pymolwiki.org/index.php/Retain_order http://www.pymolwiki.org/index.php/Pymolrc Cheers, Thomas On 22 Apr 2015, at 20:39, Spencer Bliven sbli...@ucsd.edu wrote: I'm working on a script which involves joining two objects together, which I do using the create command. The input objects have different chain identifiers, but identical residue numbers. When I create the joined object, I would expect all atoms from the first object to be added, followed by all atoms from the second object (with atom IDs being unchanged for the first object, and then continuing sequentially for the second object). Instead, the produced object alternates between atoms of each of the input objects: PyMOLiterate joined, print (ID,chain,name) (0, 'A', 'N') (1, 'B', 'N') (2, 'A', 'CA') (3, 'B', 'CA') (4, 'A', 'C') (5, 'B', 'C') (6, 'A', 'O') (7, 'B', 'O') ... This order breaks cartoon and ribbon representations, as well as makes the sequence view display each atom individually rather than combining residues. A somewhat convoluted but reproducible case follows (Using MacPyMOL 1.7.4): fetch 4rp9, type=pdb1 split_states 4rp9 alter 4rp9_0002, chain = 'B' create joined, 4rp9_* and resi 282 I've tried various combinations of the rebuild and sort commands, as well as manually changing the IDs of the objects, but I haven't been able to find a workaround yet. Sort seems to operate on the resi and ignores the ID chain. Is this a bug or am I doing something wrong? Thanks, Spencer -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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
