[Chimera-users] Truncating fitted structures using a map mask

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 20 14:28:32 PDT 2018

Hi Ahmad,
If you can select just the atoms you want, then you can easily save them.  For example, you could select the dimer and then select additional atoms (or whole residues) within a zone of the dimer.  You could hide the remaining atoms or delete them. You could also save all selected atoms to a file without deleting or hiding the others (see options in File… Save PDB).  However, it may be simplest to delete them and then either just save the session or save all the atoms to a file.  If you’re saving them to a PDB file and they are comprised of more than one model, it may be best to combine them into a single model first (see “combine” command or “copy/combine” function in the Model Panel).

There are lots of ways to select the dimer in the first place: with the mouse, or commands, or the menu. Exact command depends on whether the  monomers are in different models or are just different chains within the same model.  For example if they are chains A and B in model #1,

select #1:.a-b

You could then use Select… Zone in the menu or just use a command to select the whole zone in the first place, e.g.

select #1:.a-b z<5

for whole residues with any atom within 5 A of the A,B chains in model #1.  
I hope this helps
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 20, 2018, at 8:14 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Hello,
> I have a tubulin lattice (sheet) fitted into a microtubule map. I want to generate a structure that has only one dimer, surrounded by only fragments from the other dimers on the top, bottom and sides. 
> Is there a way to do that in chimera? 
> Regards. 

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