[Chimera-users] select all side chains

Zhou, Ming (NIH/NCI) [C] zhouming2 at mail.nih.gov
Mon Dec 9 11:48:55 PST 2013


Hi Elaine, thank you so much for your quick response. I actually is trying to do a simple energy minimization on the side chains. I can't combine the minimize command and the spec-atom command in the command line. Is there a way to do that?

Minimize spec #0:

The command line won't take the spec-atom selection I put in after : 

Thanks

Ming

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Monday, December 09, 2013 2:40 PM
To: UCSF Chimera Mailing List
Cc: Zhou, Ming (NIH/NCI) [C]
Subject: Re: [Chimera-users] select all side chains

Another note:
If you are using this for coloring, even though only the sidechain atoms are selected, the ribbon for those residues would still also be colored unless you use ",a" in the coloring command, or if using the Actions menu, choose "Actions... Color... all options" and in the resulting dialog set "Coloring applies to" to "atoms/bonds" instead of "all of the above."

(I noticed a question you had asked earlier and it reminded me of this issue!) <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006343.html>

Elaine

On Dec 9, 2013, at 11:29 AM, Elaine Meng wrote:

> Dear Ming Zhou,
> There are a few different ways, but one is to select protein atoms that are NOT backbone, e.g.:
> 
> select protein & ~@n,ca,c,o
> 
> Another way is with the command:
> select side chain/base.without CA/C1'
> 
> ... or the shorter version:
> select without CA/C1'
> 
> This is because you can use various Select menu entries exactly as they appear in the menu to specify atoms in the command line.  The menu includes "Select... Structure... side chain/base... without CA/C1'"  For more details on which menu items can be used in this way, see the section on "built-in classifications":
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec
> .html>
> 
> If there was also DNA/RNA in the structure, you could then use an additional command to de-select just that part:
> ~select nucleic acid
> 
> There is also a "with CA/C1'" (instead of "without") for example if you wanted to use the selection to display the side chains connected to ribbons instead of floating in space.
> 
> 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 Dec 9, 2013, at 10:34 AM, Zhou, Ming (NIH/NCI) [C] wrote:
> 
>> Dear Elaine: 
>> I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? 
>> Thanks
>> Ming Zhou
> 




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