[Chimera-users] on color zone

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 17 08:57:08 PDT 2015


Dear Smith,
The main thing is how to select or specify the set of atoms in each fragment.  Then you can color each of those sets of atoms a different color.  When that is done, then select all the atoms, use Color Zone, and then split.  However, it is impossible to give exact instructions of how to select or specify only the atoms in a fragment without knowing how tthey are described in your PDB file.  If you know that one fragment consists of residues 12-58 of chain A, then one way to select it would be to use command:

select :12-58.A
… then color using Actions menu, or, just use a command to do the whole thing without selecting:
color orange :12-58.A

Another way to select a range of residues would be to show a sequence window (Favorites… Sequence, choose chain of interest) and then click-drag to select a range of residues in the sequence window, which will also select them in the 3D structure.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 17, 2015, at 8:24 AM, "Smith Liu" <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> I have a mrc file for a protein complex with a 3-fragment sheets (from A to B, from B to C, from C to D, and they were connected by H-bonds). Will you please  introduce to me on how to use color zone to split to get the mrc file for each fragment of the sheets? I have tried to do it by myself, however I find the splitting was not  done based on fragment, i.e., I cannot get the mrc file for each fragment of the sheets.
> 
> I am looking forward to getting your reply.
> 
> Smith




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