[Chimera-users] Selection through bond and fragment naming

[Elaine Meng]

Hi JD,
If one fragment = one residue, all your problems are solved!  Unfortunately, xyz may not have any notion of "residues," so that sounds like the hard part:  either pre-processing to create PDB files in which each fragment is a residue, or making it happen within Chimera using python scripting.  Tom Goddard may have an idea, as he recently added functionality that looks at connected groups of bonds.

I can only describe the easy part, after each fragment is a residue:

If you select part of a residue such as an atom or bond, then pressing keyboard up arrow or using command "select up" will expand the selection to the whole residue. 

Attributes are easily set for whole residues, for example with command "setattr" (one value at a time) or with "defattr" and an attribute definition file (multiple values at a fime). 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html>

The first example attribute definition file defines a residue attribute.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>

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 Mar 11, 2011, at 7:42 AM, Jean Didier Pie Marechal wrote:

> Hi, 
> I have a system from which I only have xyz coordinates. What I would like to do is to define myself residue attribute on different fragments of the molecules. Could you tell me how (or if there is a way to ):
> 
> 1. expand a selection to bonding atoms (i.e. I click on one atom and expand selection through one bond after each actions) This would be of the easiest way for me to select the fragments I want to.
> 2. set a residue attribute to the given selected fragment. I think I remember how to do so in scripting, but what is the command line to do so?
> 
> Kind regards, 
> 
> JD
>