[Chimera-users] PDBFILE statistics

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 4 09:14:22 PDT 2011

Hi Alex,
There is nothing exactly like that.  However, you could just count oxygens, nitrogens, subsets of residues etc. by making a selection and seeing how many atoms or residues are selected.  

You could make a selection with commands, for example
select O
...would select all oxygens
select protein
...would select all protein
select :trp
... would select all tryptophan residues

or with the menu, for example
Select... Chemistry... element... O
Select... Structure... protein
Select... Residue... TRP

Then after something is selected, you could see contents of the selection (how many atoms and residues) by clicking the green  magnifying glass near the bottom right corner of the Chimera window, or write a list of the selected atoms or residues to a file or to the Reply Log (Actions... Write List).   The status line also reports the number of selected atoms, temporarily.

If instead you meant small molecule descriptors (cheminformatics), Chimera does not calculate these for the most part, and other programs would be more suitable.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 4, 2011, at 6:21 AM, Alex Shkumatov wrote:

> Hallo
> I wonder if there is a command in Chimera to show the statistics of the 
> PDBFILE, i.e.
> number of oxygens, nitrogen atoms, number of rotamers, etc..
> Thank you in advance
> Alex

More information about the Chimera-users mailing list