[Chimera-users] zones and residue name/number

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 25 08:50:55 PDT 2010

Hi Francesco,
If you want to see the full VDW size of those residues, use the sphere  

You can also specify any one by residue number and chain ID, for example

select :342.A z<5.0

I don't know what the issue is with your structure or what you mean by  
"did not work" but perhaps the easiest way for you would be just to  
select that atom (Ctrl-click in the graphics window) and then use  
"sel" to specify it:

select sel z<5.0

I'm not aware of any use of PSF/DCD in Chimera except as trajectory  
input.  What do you mean?  Writing it out?
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 25, 2010, at 1:42 AM, Francesco Pietra wrote:

> Hi:
> I was trying to detect all residues (or atoms) within a given distance
> from a single-atom ligand in model #0 (PDB file). There are several
> such single-atom ligand atoms in model #0 (practically invisible in
> chimera as they are not shown at their relative vdw size), each
> specified  by different residue and atom numbers. I want to carry out
> the task for each single-atom residue. Therefore I can't use the
> standard command
> select #0:single-atom-ligand z(or za)<given.distance
> because that applies to all those single-atom-ligands.
> Unless the residue can be specified differently (the residue number in
> place of residue name did not work), the only way that I found to come
> out was to set different names for the different single-atom ligands.
> Is anything better?
> Secondary question: is there any plan to support psf/dcd format (which
> I am now using for MD with namd) beyond reading movies?
> Thanks
> francesco pietra
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