Re: [PyMOL] about Display CCP4 Maps
Hi Lina, Could you be more specific about what you are trying to do. E.g. I have a structure from the pdb and I would like to display the density. If it is this option then you can automatically generate ccp4 type maps from http://eds.bmc.uu.se/eds/ assuming the structure factors have been deposited. You can them load these into pymol (file.ccp4) Or I am determining the structure of a protein ligand complex and I wish to calculate the electron density map . If this is the case I would suggest some further reading of the ccp4 tutorials. These come with ccp4i Hope this helps Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -Original Message- From: lina [mailto:lina.lastn...@gmail.com] Sent: Wednesday, 26 October 2011 1:27 a.m. To: Thomas Holder Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] about Display CCP4 Maps On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder spel...@users.sourceforge.net wrote: Hi Lina, do you already have any electron density or reflection file (*.map, *.mtz, ...) or do you want to create a fake density from your structure? It's not I don't have the reference electron density file. mainly wish to calculate a density map based on the structure? clear from your question. Cheers, Thanks for asking. Thomas On 10/25/2011 10:28 AM, lina wrote: Hi, I went through the pymolwiki and cross this page: http://www.pymolwiki.org/index.php/Display_CCP4_Maps I have some questions: 1] do I need generate the map from ccp4 (I have already installed the ccp4i, but seems not easy to know how to get the map) 2] For small molecular (ligand), the ccp4 is the best way to obtain its electron density map? Seems those questions are not so-pymol-related, but I wish if someone are familiar with this, can give me some advice?? Those questions might be easy, but to me at present it seems very confusing. Thanks with best regards, -- 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 -- 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] how to activate pymol from remote server
Hi Thomas, Troels and Alvin, I appreciate your instant and detail advices to my problem, I got succeeded - scripting in [C] enabled activate pymol in [S]. As Troels says, I agree it's not pymol issue indeed, and sorry for contaminating some questions to here list. What is done: laptop$ ssh -l (loginName) (remote-machine) # tried ssh -Y or -X, but simply this succeeded login@(remote-machine)$ export DISPLAY=:0.0# it seemed the point, somehow not enough laptop:0.0 login@(remote-machine)$ xclock #worked login@(remote-machine)$ pymol #worked Referred from: laptop# xhost +remote-machine laptop# ssh -l loginName remote-machine login@remote-machine# export DISPLAY=laptop:0.0 login@remote-machine# xterm - see if it works login@remote-machine# pymol More I want to quit pymol GUI from [C], but 'pymol -qip' will be fit as Thomas says. Thanks again for all. Regards, Masataka -- 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
