[Chimera-users] problem with huge PDB atom numbers

Samuel Coulbourn Flores scflores at stanford.edu
Sun Feb 14 13:00:02 PST 2010

Hi Guys,

I thought I'd point out a problem with Chimera's atom numbering.  I am working on a ribosome model which has about 50 chains.  The ribosome pushes the limits of the PDB format;  the five columns reserved for atom numbers are not sufficient to give each atom a unique atom number.  This is not typically a problem for me, I just start the atom numbering at 1 for each chain.  However chimera doesn't do this, it tries to assign sequential, unique numbers to each atom and ends up spilling over onto column 6, which is in the record name field.  This wreaks havoc with other programs which I use to process the PDB files that chimera puts out.  I am manually renumbering to deal with the issue, but the developers should think about a more permanent solution.


On Feb 14, 2010, at 12:41 PM, Elaine Meng wrote:

> On Feb 14, 2010, at 11:31 AM, Thiruvarangan Ramaraj wrote:
>> Hi Elaine,
>> I am working on calculating the Solvent accessible Surface Area on the antigen interaction region. I am confused about adding/removing hydrogen's, my question is will there be a change in SASA if you have or not have  hydrogen's atoms added.
>> Thank You.
>> -Thiru
> Hi Thiru,
> Yes, it will be different with and without hydrogen, because the molecule is treated as a set of spheres where each atom is a sphere.  There will be more small bumps on the surface when there are hydrogens.  Also, the radii of the other atoms may change because there are different defaults for structures with and without hydrogens, as described here:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html>
> I think surface area calculations are usually done on structures without hydrogens.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                     http://www.cgl.ucsf.edu/home/meng/index.html
> P.S. you may want to use "measure buriedArea" (or maybe you are already doing that):
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
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