[Chimera-users] Deleting parts of secondary structures

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 3 09:17:30 PDT 2009

Dear Andy,
There is a "language" for specifying atoms, residues, chains, models  
in commands.  For example:

delete #0:10-20.a,12.b,40.b
(delete residues 10-20 in chain A and residues 12 and 40 in chain B,  
all in model 0)

~ribbon #0:312-456
(hide ribbon for residues 312-456 in all chains of model 0)

~disp :.a
(undisplay atoms/bonds for chain A in all models)

There are many fancier things you can do, including distance zones,  
etc., and it is all documented:

There are also some examples of command-line specifications on the  
second page of the Quick Ref:

Another more graphical possibility is to show the sequences of the  
various chains (Favorites... Sequence) and select parts of those,  
then use the Actions menu to delete atoms/bonds, or hide atoms/bonds,  
or hide ribbons.

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

On Jun 2, 2009, at 11:22 PM, Anindito Sen wrote:

> Dear All
> I have a Chimera session in which I have 6 sets of PDB files  
> (ribbon representation) showing variability in the structures.  
> However I wish to display only few of the subunits. Questions are:
> 1. How do I delete undesired subunits from all the chains on the  
> command line
> 2. How do I select particular residues from specific chains (not  
> all the 6).
> Thanks
> Andy

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