[Chimera-users] zones and residue name/number

Francesco Pietra chiendarret at gmail.com
Thu Mar 25 01:42:24 PDT 2010


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?

francesco pietra

More information about the Chimera-users mailing list