Hi Jason Thanks for your detailed reply and for pointers on the iterate command for mapping the bfactors.
I think I understand whats going on and there was a fault in my understanding i.e I was wrong. Even though my script puts the conservation record as b-factor to all atoms of any given residue . If I say color surface by spectrum b-factors *.ca , pymol colors only the calpha atoms by the range of b-factors ( 0 to 11). The remainder non-calpha atom surfaces still have their default cpk based color. I conveniently assumed the command color surface by spectrum b-factors *.ca would have colored all the residues in the surface representation by the value of the b-factor for their corresponding c-alpha atom. In my case when I then used color by bfactors ( all atoms in object by implication). The hetatoms were getting dragged into the definition for all atoms and skewing the range. I was wrong in that the range was misreported. Thanks for the clarification. hari On Tue, Jul 5, 2011 at 2:42 PM, Jason Vertrees <jason.vertr...@schrodinger.com> wrote: > 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
