Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries
Hi Robert, this solves exactly my problem and gives me the pictures I wanted. Thank you very much for the quick answer! Cheers, Alexander Am Mittwoch, den 26.10.2011, 09:48 -0400 schrieb Robert Campbell: Hi Alexander, On Wed, 2011-10-26 12:53 EDT, Alexander Schulz sch...@dwi.rwth-aachen.de wrote: Hi Thomas, thank you very much for the answer, I'm beginning to understand the actual problem now. dss state=1 helps, but it changes the problem: I would like to see the secondary structure that corresponds to the single snapshot. When I use dss state=1, I just see the secondary structure of the first snapshot in all snapshots. Is there a way to calculate the secondary structure for each individual snapshot stored in this single .pdb file? Yes, simply load the pdb file with the discrete=1 flag: load md_file.pdb, discrete=1 dss md_file Setting the discrete flag causes PyMOL to store more information (B-factors, secondary structure) with each atom of each state -- so it can also be noticeably slower to load and uses more memory. Cheers, Rob -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ 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] Pymol: Cartoon representation for .pdb file with multible entries
Hi Alexander, by default PyMOL recognized secondary structure as the minimum consensus over all states. So if a residue is not recognized as helix or sheet in _all_ states, it will be assigned as loop. You might be happy with this: # type after loading the file dss state=1 For detailed explanation what values are valid for the state argument see the PyMOLWiki page: http://pymolwiki.org/index.php/Dss Cheers, Thomas On 10/26/2011 11:04 AM, Alexander Schulz wrote: Hi everyone, I'm quite new to Pymol and I hope that I don't ask something that has been answered several times before, but I didn't find anything about this topic that could solve my problem. I've prepared a .pdb file containing one protein at different times in the simulation. I'd like to prepare a video from this file, which is why I'd like to keep everything in one .pdb file. When I select cartoon as a representation, the backbone is visualized as a tibe (as always), but no secondary strucutres are recognized. When I copy one of the snaphots out of the .pdb and open in seperately, the secondary structure is shown correctly. How can I make Pymol show the structure of the multible states in one file correctly? Thanks in advance for answers! Cheers, Alexander -- Thomas Holder MPI for Developmental Biology -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ 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] Pymol: Cartoon representation for .pdb file with multible entries
Hi Thomas, thank you very much for the answer, I'm beginning to understand the actual problem now. dss state=1 helps, but it changes the problem: I would like to see the secondary structure that corresponds to the single snapshot. When I use dss state=1, I just see the secondary structure of the first snapshot in all snapshots. Is there a way to calculate the secondary structure for each individual snapshot stored in this single .pdb file? Cheers, Alexander Am Mittwoch, den 26.10.2011, 12:18 +0200 schrieb Thomas Holder: Hi Alexander, by default PyMOL recognized secondary structure as the minimum consensus over all states. So if a residue is not recognized as helix or sheet in _all_ states, it will be assigned as loop. You might be happy with this: # type after loading the file dss state=1 For detailed explanation what values are valid for the state argument see the PyMOLWiki page: http://pymolwiki.org/index.php/Dss Cheers, Thomas On 10/26/2011 11:04 AM, Alexander Schulz wrote: Hi everyone, I'm quite new to Pymol and I hope that I don't ask something that has been answered several times before, but I didn't find anything about this topic that could solve my problem. I've prepared a .pdb file containing one protein at different times in the simulation. I'd like to prepare a video from this file, which is why I'd like to keep everything in one .pdb file. When I select cartoon as a representation, the backbone is visualized as a tibe (as always), but no secondary strucutres are recognized. When I copy one of the snaphots out of the .pdb and open in seperately, the secondary structure is shown correctly. How can I make Pymol show the structure of the multible states in one file correctly? Thanks in advance for answers! Cheers, Alexander -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ 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] Pymol: Cartoon representation for .pdb file with multible entries
Hi Alexander, On Wed, 2011-10-26 12:53 EDT, Alexander Schulz sch...@dwi.rwth-aachen.de wrote: Hi Thomas, thank you very much for the answer, I'm beginning to understand the actual problem now. dss state=1 helps, but it changes the problem: I would like to see the secondary structure that corresponds to the single snapshot. When I use dss state=1, I just see the secondary structure of the first snapshot in all snapshots. Is there a way to calculate the secondary structure for each individual snapshot stored in this single .pdb file? Yes, simply load the pdb file with the discrete=1 flag: load md_file.pdb, discrete=1 dss md_file Setting the discrete flag causes PyMOL to store more information (B-factors, secondary structure) with each atom of each state -- so it can also be noticeably slower to load and uses more memory. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ 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
