[Chimera-users] active questions

Arthur Szabo agszabo at outlook.com
Mon Apr 3 13:26:02 PDT 2017


Thank you 

Very helpful as always.


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Monday, April 03, 2017 3:20 PM
To: Arthur Szabo <agszabo at outlook.com>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] active questions

Hi Arthur,
You could try Ctrl-click on some atom to select it and then keyboard up arrow to promote selection to the whole residue.

You should also be able to see in the pop-up temporary label when you mouse over some atom its residue number and chain ID, which you could specify in the command line.  For example if residue 10 in chain A,

select :10.A

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

> On Apr 3, 2017, at 11:21 AM, Arthur Szabo <agszabo at outlook.com> wrote:
> I am working with a structure that is largely a protein, and there is a short oligonucleotide associated with it. In the tools  menu the sequence of the protein is Chain A and the short oligonucleotide is Chain C. I have shown their respective sequences. I also know how to highlight components of each chain etc. 
> However, there is a short dinucleotide with two thymine residues that are also part of the structure. I was able to select these residues and the two thymine residues in the oligonucleotide by using the SELECT menu: residues: dT. So in total four thymine residues are selected and with the ACTIONS menu I can visualize them. Going to Chain C I can hide the two thymine residues on the longer oligo.
> How can I select the other two thymine residues that make up the short dinucleotide?
> One of these thymines is covalently bound to a tyrosine residue through a phosphodiester bond. I can visualize the tyrosine monophosphate through Chain A, and one can see it  connected to the relevant thymine residue.
> But I  would like to color the two thymine residues. But I cannot select them or at least I do not know how to select them.
> I am not an expert at using the command line. Likely there is something there.
> Again your assistance is sincerely appreciated.
> Arthur G. Szabo

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