[PyMOL] SS in a trajectory
Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot. --Jianghai -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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] SS in a trajectory
If none suggests a solution in PyMOL ten use sscache.tcl script in VMD to update the SS at every frame. Thomas On 24 April 2013 17:31, Jianghai Zhu j...@idi.harvard.edu wrote: Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot. --Jianghai -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] SS in a trajectory
Hi, On Wed, 2013-04-24 10:31 EDT, Jianghai Zhu j...@idi.harvard.edu wrote: Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot. When you load the trajectory, use the discrete flag to have PyMOL computer the secondary structure for each state . load trajectory.pdb, discrete=1 I'm assuming you are loading a multi-model .PDB file as the trajectory. If you are using the load_traj command to load an AMBER trajectory, there is no similar option. 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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
