Dear Elaine and all,

Thank you for your answer!

I just need to specify – will that method also work for the sequences (not only on the atom level)?

The main aim is to see which sequence is out of the cryo-map and by hand check and list them down (to correct the ones that out later).

I tried to open the sequence menu and do that by hand, but the model is quite big.

I hope the method you kindly shared will do that semi-automatically.

Sincerely,

Dmitry

Sent from Mail for Windows 10

From: Elaine Meng
Sent: Friday, March 13, 2020 7:01 PM
To: Dmitry Semchonok
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Getting the analysis of the side chains that are not in the density map

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@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