Hi Hari, > I am using svn pymol rev 3953 on a 64 bit Ubuntu box. > I have a custom script that maps extent of conservation into the > b-factor record of a pdb for visualization. > > I noticed a small feature in pymol > > My protein atoms in chain A have b-factors from 0 to 11 to indicate > conservation extent , . The Heteroatoms , in this pdb also in chain A > have their ususal b-factors in the 60s. > Now if I ask for the surface to be colored by bfactors spectrum for *.ca. > > Pymol echoes > > > Spectrum: range ( 0.00000 to 11.00000).
We can quickly test the ranges to ensure PyMOL is acting appropriately: withHET, withoutHET = [], [] iterate *, withHET.append(b) iterate n. CA, withoutHET.append(b) # print range w/HET print min(withHET), max(withHET) # print range wout/HET print min(withoutHET), max(withoutHET) and we can color by: # color by spectrum spectrum b, rainbow, n. CA The problem I think you're having is that the colors don't expand to the surface as you want. I created a script awhile back to do just this; see http://www.pymolwiki.org/index.php/Expand_To_Surface. Please let us know if this helps. Cheers, -- Jason > > But the colors on the surface clearly also include the heteroatoms > .which are all above 55 and in chain A. > So the whole protein surface ends up blue since majority of values are below > 11. > > I did get around this by removing the heteroatoms to a different chain > . But it seems there is a discrepancy between what is echoed to the > stdout and the color-range pymol displays on the screen in this > instance. > > Hope this is not some setting that I am messing up on my side > > Thanks > hari > > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ 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
