[Chimera-users] question about specific protein display

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 13 13:08:55 PDT 2020

Hi Giulia,
First you have to decide how to divide the structure, e.g. figure out lists/ranges of residue numbers that will be in part 1, everything else in part 2.

Open the structure and split it, specifying this list of residues.  For example, command

open mystructure.pdb
split atoms :20-46.A,200-350.A

... to put residues 20-46 and 200-350 of chain A in one part, everything else in the other.  (If you don't need anything for your figures except the protein, it may be simpler to delete all nonprotein parts first, e.g. command "delete ~protein" before the split command.)

See explanation of "split" command:

Then see this "opened interface" image tutorial for ideas on how to make a figure showing the interior.  You can generalize, i.e. you don't have to follow all the steps, just the ones that do the things you want like positioning the two parts, and you could use different display styles (spheres rather than molecular surface, for example), coloring, etc.

There are lots of tutorials including "getting started" if you don't know how to change display styles, colors, etc.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 13, 2020, at 9:06 AM, Galotto, Giulia <ggalotto at wpi.edu> wrote:
> Hi, 
> I am using Chimera to display a protein domain in my paper. 
> The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed.
> Could you guide me on how to do this?
> Thank you so much for your help! 
> Best, 
> Giulia Galotto
> PhD Student 
> Vidali Lab
> Worcester Polytechnic Institute

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