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

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 13 12:44:28 PDT 2020

Hi Dmitry,
I don't know exactly what you mean by "work for the sequences"  although the answer is probably yes, there are various ways to get to the residue level.

If you select even just one atom in a residue, that residue will also show up as selected with a green box in the Sequence window (Multalign Viewer).   

Further,  if you select a set of atoms (for example by attribute value) and then hit up arrow on the keyboard, it wll promote the selection to their whole residues.

Even if you don't "promote" the selection to whole residues there is a choice in Actions... Write List dialog to simply write a list of the residues that contain a selected atom rather than every single individual atom.  This capability is also available as the "writesel" command if scripting is better for your workflow.  

I hope this helps,

> On Mar 13, 2020, at 12:20 PM, Dmitry A. Semchonok <semchonok at gmail.com> wrote:
> 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 at 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 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

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