[Chimera-users] Getting the analysis of the side chains that are not in the density map

[Elaine Meng]

Hi Dmitry,
There may be more than one way, but the way I imagine is to assign each atom the local density value, and then select atoms by those values.  Your cutoff for selecting atoms could be the same as the level at which you are contouring the map. You can list the selection in the Log, or write out a PDB file of the selected atoms, etc.

You can assign the values with the "Values at Atom Positions" tool (in menu under Tools... Volume Data) or the command "measure mapValues":
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues>

Then you can select atoms above or below some value of that attribute with the Render/Select by Attribute GUI (in menu under Tools... Depiction) or with command-line specification by attribute value, e.g. something like this if the attribute was named "value_mymap":

select @/value_mymap>0.25

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

The set of selected atoms can be written to the log (Actions... Write List) or saved as PDB (Actions... Write PDB):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuactions>

You could also save a list of the atoms with their values from the Render/Select by Attribute dialog, see "saving attributes"
<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 Mar 13, 2020, at 9:42 AM, Dmitry Semchonok <Semchonok at gmail.com> wrote:
> 
> Dear colleagues,
> I have a map with the fitted model inside.
> Some of the side chains are out for the density map.
> 
> I want to have a get a file where the side chains that are not in the density map are listed.
> Does anyone know how to do that?
> 
> Thank you!
> Sincerely,
> Dmitry