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 > > > On Apr 6, 2011, at 4:22 AM, Ramiro Téllez Sanz wrote: > >> Hi and thanks for reading this. >> >> I have googled for a way to achieve what I want and have gone through >> the wiki, to no avail. >> >> I would like to color in a different way the different helix types: >> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get >> distinct colors for each type by default. But if the same pdb file is >> open with PyMOL all helices are treated the same way. Can't PyMOL >> distinguish helix types? >> >> Thanks in advance, >> Ramiro Téllez Sanz >> Dept. Physical Chemistry >> University of Almeria >> Spain >> >> ------------------------------------------------------------------------------ >> Xperia(TM) PLAY >> It's a major breakthrough. An authentic gaming >> smartphone on the nation's most reliable network. >> And it wants your games. >> http://p.sf.net/sfu/verizon-sfdev >> _______________________________________________ >> 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 > > * > *art*/for/*science* > > *H. Adam Steinberg* > Artist, Scientist, Developmental Editor > > www.artforscience.com <http://www.artforscience.com> > 7904 Bowman Rd > Lodi, WI 53555 > 608/729-5944 > > * > > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > > > > _______________________________________________ > 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 ------------------------------------------------------------------------------ Forrester Wave Report - Recovery time is now measured in hours and minutes not days. Key insights are discussed in the 2010 Forrester Wave Report as part of an in-depth evaluation of disaster recovery service providers. Forrester found the best-in-class provider in terms of services and vision. Read this report now! http://p.sf.net/sfu/ibm-webcastpromo _______________________________________________ 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
