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 > 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 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
[PyMOL] Pymol: Cartoon representation for .pdb file with multible entries
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
