[Chimera-users] Quantification of electron density volume

Elaine Meng meng at cgl.ucsf.edu
Sat Jan 27 09:06:36 PST 2018


Dear Priyamvada,
Yes, you can save the atom attribute values (which Values at Atom Positions assigns) from the Render/Select by Attribute dialog.  This dialog is the one showing the histogram of values, but you can also open it from the main menu: Tools… Structure Analysis… Render by Attribute. You can save the values to text file using the dialog’s menu as described here, “saving attributes” near the bottom of the page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

If you really wanted to overwrite the bfactor, you’d have to save the attribute file as mentioned above, text-edit it to change the name of the attribute to bfactor, and then read it back in with Define Attribute or command “defattr” as described in this previous post to the list, and then save a copy of the PDB file now with the different bfactor values.  However, the bfactor column is narrow, so the values would get rounded off somewhat.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-August/010235.html>

You can also calculate sums over sets of atoms with Attribute Calculator. See the list of things that can be done with attribute values:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 26, 2018, at 11:30 PM, Priyamvada Acharya <pacharya at nysbc.org> wrote:
> 
> Hi everyone,
> I am wondering if there is a way to extract the values plotted under Tools > Volume Data > Values at Atom Positions?
> 
> Specifically, I would like to quantify the electron density surrounding a domain and compare it to another domain. This can be easily done if the values in the Histogram plotted under the tool mentioned above can be tabulated on a per-atom basis (perhaps within a PDB file, in the B-factor column).
> 
> If anyone knows other methods to achieve this goal, that would be helpful as well.
> 
> Thank you very much in advance for your feedback and suggestions!
> Best regards,
> Priyamvada
> 




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