Hi, just for your information, the "DSSP plugin for PyMOL" has been updated to "DSSP & Stride plugin for PyMOL" :-)
The plugin generates a selection for each SSE type assigned by DSSP or Stride. Using the brilliant "copy to object" function of PyMOL, you can make two copies of protein fragments of the same SSE defined by DSSP and Stride respectively and compare them visually ! The plugin also accepts (correct) PyMOL selection expressions as input beside selection/object names. Thanks for Thomas Holder for the suggestion! Your feedback and suggestions are always welcome! cheers,hongbo On 04/12/2011 04:22 PM, Hongbo Zhu wrote: > Hi, if anybody is still interested in the topic, I have made a DSSP > plugin for running DSSP and coloring proteins according to the DSSP > secondary structure assignment. Please have a look at: > > http://www.pymolwiki.org/index.php/DSSP > > This plugin invokes DSSP (presuming you already have DSSP binary on your > hard drive) and reads the output using BioPython. It then makes several > selections, each for a kind of secondary structure elements (SSE) if > there is at least one residue in the input selection is assigned with > the SSE. > > regards, > hongbo > > On 04/06/2011 04:34 PM, H. Adam Steinberg wrote: >> Hi Ramiro, >> >> Like you, I would love to see secondary structure colored by helix type. >> Jmol however does not show this as a default. Do you know what steps you >> took to get Jmol to show secondary structure colored by helix type? >> >> I can't seem to find that setting in any of the menu options. >> >> style/scheme/cartoon >> color/structure/cartoon/By Scheme/Secondary Structure >> >> This shows all of the helices in the same color. >> >> Adam >> -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de ------------------------------------------------------------------------------ Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails _______________________________________________ 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
