[PyMOL] color surface by bfactor discrepancy between range reported on shell and range used
Hi, 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 ( 0.0 to 11.0). 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
Re: [PyMOL] color surface by bfactor discrepancy between range reported on shell and range used
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 ( 0.0 to 11.0). 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
Re: [PyMOL] color surface by bfactor discrepancy between range reported on shell and range used
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 ( 0.0 to 11.0). 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
