[Chimera-users] Selection through bond and fragment naming

Tom Goddard goddard at sonic.net
Fri Mar 11 10:29:32 PST 2011

Hi JD,

   This sounds hard.  When you open your atoms.xyz file you get a 
molecule with all atoms belonging to one residue.  Your idea to select 
an atom and then press a key to extend the selection to the atoms 
connected one-bond away sounds useful.  You could select an atom at the 
tip of the residue and then click the key several times until it reaches 
the backbone.  We don't have that.  There is a keyboard shortcut "sc" 
that selects all atoms that are connected by any number of bonds to the 
already selected atoms.  I could add a keyboard shortcut that extends 
just one bond.  Another idea is that you select one backbone bond 
between each pair of residues (ctrl-click then shift-ctrl-click) and 
delete all those bonds (Actions / Atoms&Bonds / delete).  Then each 
residue is a separate connected set of atoms.  Then the "sc" shortcut or 
a script that finds connected groups of atoms could help.

   But then you get to problem number 2, how to say those groups should 
each be a residue.  As far as I know you cannot select atoms and then 
make them a separate residue in Chimera.  Maybe you mean you will assign 
an atom attribute, write out those attributes and then process that 
result to make a PDB file?  I'm assuming your goal is to turn this set 
of coordinates into a PDB file.  You can set attributes of atoms in 
Chimera using for example

     setattr a rtype A123 sel

to set an attribute named "rtype" to A123 for all currently selected 
atoms.  What residue an atom belongs to in Chimera is not an attribute 
though.  There is a separate residue object and I don't know of a way to 
place selected atoms in a newly made residue.  Eric Pettersen would have 
the definitive answer on whether that is possible.  Of course it is 
possible with Python.


> 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
> Dr. Jean-Didier Maréchal
> Lecturer
> The Computational Biotechnological Chemistry Team
> Unitat de Química Física
> Departament de Química
> Universitat Autònoma de Barcelona
> Edifici C.n.
> 08193 Cerdanyola (Barcelona)
> Tel: +34.935814936
> e-mail: JeanDidier.Marechal at uab.es
> www: http://asklipio.qf.uab.es
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list