[Chimera-users] Double structure while loading the pdb file

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 23 16:19:32 PDT 2014

Dear Sanjeev Sariya,
There are 2 copies of the protein in this structure, plus glycosylations, water, ions, etc.  This is just the contents of the PDB file.  If you look at the page at the RCSB PDB for this structure:


… it says there are 2 chains of rhodopsin, A and B.  Any display program will show both chains when you open the PDB file, but you can hide or delete parts of the structure (such as one chain) as you wish.  For example, in Chimera you could use menu:

Select… Chain… B
Actions… Atoms/Bonds… delete

to delete chain B.  In general, any molecular display programs will also allow showing/hiding,  coloring,  changing display style, etc. of specific residues and atoms within each chain.  For example, to color only residue 113 in chain A:

color red :113.A

There is a manual page on command-line specification:

If you are a Chimera beginner, I recomend the "getting started" tutorial on our website:

There are also several tutorials in the User's Guide, ranging from beginner to more advanced (see Chimera menu: Help… Tutorials).
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 22, 2014, at 4:58 AM, Sanjeev Sariya <s.sariya_work at ymail.com> wrote:

> Hi Members/Developers,
> I loaded pdb file 1U19- Bovine Rhodopsin.
> structure is double the length what is to be. 
> On terminal, on doing
> color red: 113
> I see that 2 residues are colored.
> Why there are 2 molecules in same file?
> How do I hide one molecule?

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