Re: [PyMOL] Downloading the biological assembly from the PDB
Hi Martin, you may also consider these scripts from PyMOLWiki that generate the biological assembly from the asymmetric unit. http://pymolwiki.org/index.php/BiologicalUnit/Quat or http://pymolwiki.org/index.php/BiologicalUnit Cheers, Thomas Martin Hediger wrote, On 05/03/11 22:00: Dear all I would like to ask how it is possible to download the coordinate file for the biological assembly of a protein structure from the PDB. Naturally, this is not a question directly related to PyMOL, but I thought I'll be reaching at least a couple of Biochemists/Chrystallographers who know how to do this. As an example, when downloading the PDB file of 1AVD, I get a file with two chains. The biological assembly would be a tetramer, so I wonder what URL I would require to write into a script that does the downloading. Thanks for help on this. Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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] Fetching scripts
Hi all, I'm considering building in a mechanism for automatically fetching scripts from the PyMOL Wiki. The goal is to allow users to say fetch findSurfaceResidues, type=script findSurfaceResidues doShow=True, cutoff=0.5 The convenience benefits are obvious, especially for new users, and I think that lowering the barrier to script usage will greatly increase both the number of people who use various scripts and the incentive to place scripts on the wiki (especially if the fetch mechanism makes it easy for script authors to provide a citation/DOI/etc.). I've put up a tentative page about this on the wiki ( http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments either via the list, private email or on the wiki, especially about - whether you think it's a good idea - security and validation - options you'd like - implementation issues The plan is to write this as a userland script first. If issues relating to security and validation can be resolved, we'll see if the official builds want to include it. Cheers, -Michael -- 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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] Fetching scripts
Sounds awesome! Adding an option to chose whether to load the script every time PyMol launches, or just fetch and use it once, would be even more convenient. It would resemble installation of packages from Linux repositories ;) On 4 May 2011 18:59, Michael Lerner mgler...@gmail.com wrote: Hi all, I'm considering building in a mechanism for automatically fetching scripts from the PyMOL Wiki. The goal is to allow users to say fetch findSurfaceResidues, type=script findSurfaceResidues doShow=True, cutoff=0.5 The convenience benefits are obvious, especially for new users, and I think that lowering the barrier to script usage will greatly increase both the number of people who use various scripts and the incentive to place scripts on the wiki (especially if the fetch mechanism makes it easy for script authors to provide a citation/DOI/etc.). I've put up a tentative page about this on the wiki ( http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments either via the list, private email or on the wiki, especially about - whether you think it's a good idea - security and validation - options you'd like - implementation issues The plan is to write this as a userland script first. If issues relating to security and validation can be resolved, we'll see if the official builds want to include it. Cheers, -Michael -- 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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] Simultaneous fading in and out of different representations
Hi Sena, the second argument to mdo was not correct, there you had two strings and a semicolon what must be one string and the semicolon within. Works for me like this: python cmd.mset(1x100) cmd.mdo(1, set cartoon_transparency, 1.0; set ribbon_transparency, 0.0) for i in range(40,60): cmd.mdo(i, set cartoon_transparency, %f; set ribbon_transparency, %f % (1-(i-40)/20.0, (i-40)/20.0)) cmd.frame(1) python end Cheers, Thomas Rajagopalan, Senapathy wrote, On 05/04/11 19:50: Hi Everyone, I am making a movie and want to show the transition between a cartoon and a ribbon representation smoothly (fading out cartoon and fading in ribbon) . So I tried writing a simple python script like: --- for i in range(40,60): cmd.mdo (i, set cartoon_transparency,%f %( 1-(60-i)/60.0 ); set ribbon_transparency,%f %( (60-i)/60.0 ) ) --- And --- for i in range(40,60): cmd.mdo (i, set cartoon_transparency,%f %( 1-(60-i)/60.0 ) ) for j in range (40,60): cmd.mdo (j, set ribbon_transparency,%f %( (60-j)/60.0 ) ) -- And various other combinations, but none seem to produce the result that I desire. Can anyone help me with the scripting as my python knowledge is very basic. Thanks Sena -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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] Fetching scripts
Hi, From a security perspective, it seems like the ideas on the wiki page are all related to securing the remote source. It might be worth considering what could be done to minimize how much pymol has to trust the remote source or the network. A few ideas: - Sandboxing would be ideal, but I don't know if there's infrastructure in python to support it. It might be easier to filter fetched scripts to only allow a restricted subset of python functions (the ast library looks like it might make this a bit easier). If a script can't access the network or hard disk, then it doesn't need to be trusted as much. - The wiki doesn't appear to support SSL. So that means trusting the network to get to the wiki correctly, in addition to the wiki itself. I don't have any good ideas for how to work around this one. Pete Michael Lerner wrote: Hi all, I'm considering building in a mechanism for automatically fetching scripts from the PyMOL Wiki. The goal is to allow users to say fetch findSurfaceResidues, type=script findSurfaceResidues doShow=True, cutoff=0.5 The convenience benefits are obvious, especially for new users, and I think that lowering the barrier to script usage will greatly increase both the number of people who use various scripts and the incentive to place scripts on the wiki (especially if the fetch mechanism makes it easy for script authors to provide a citation/DOI/etc.). I've put up a tentative page about this on the wiki (http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments either via the list, private email or on the wiki, especially about - whether you think it's a good idea - security and validation - options you'd like - implementation issues The plan is to write this as a userland script first. If issues relating to security and validation can be resolved, we'll see if the official builds want to include it. Cheers, -Michael -- 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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
