[chimerax-users] Fitmap on a subvolume?

[Tom Goddard]

Hi Vincent,

A more direct approach would be to just fit the subregion of the first map into the second map.  You could get a subregion using the crop mouse mode or the "region" option of the volume command -- these would just give rectangular boxes.  If you wanted a different shape subregion, you could mask to a sphere (commands shape sphere, and volume mask).  Or you could use the volume zone command to take the region of the map near a fit atomic model and save that piece to a separate MRC file and fit that.

	Tom

> On Sep 27, 2022, at 9:15 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Vincent,
> (A) According to your suggestion, if you first fit (or somehow position) each PDB structure into its related map, I believe you can then use "matchmaker" to superimpose PDB 1 onto PDB 2 with the "bring" option to also move map 1 along with PDB 1.
> 
> See "matchmaker" command including "bring" option:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
> 
> (B) Another thought, if one map is like a subset of the other, is to use Segment Map on the larger map, and then use Fit to Segments to fit the smaller map to the corresponding segment.   These are tools from the Segger package included with ChimeraX:
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html>
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/fitsegments.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Sep 27, 2022, at 7:39 AM, vincent Chaptal via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi, 
>> 
>> I'd like to compare 2 maps, and would like to superposse them on specific portions of the map. 
>> Is there a way to do this? 
>> 
>> I was thinking to assign a pdb to each map, and apply a superposition of pdb1 onto pdb2 and have the maps follow the movement? 
>> 
>> Thank you
>> Vincent
> 
> 
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