[Chimera-users] zones and residue name/number

Francesco Pietra chiendarret at gmail.com
Mon Mar 29 07:25:21 PDT 2010

Hi Elaine:

Before dealing with all your suggestion, let me say that opening the
pdb file, selected HOH or SO4 can be seen at their full VDW with the
"sphere" representation. Xenon atoms - treated the same way - remain
invisible. Therefore, I extracted the Xe atoms from the pdb file,
creating a pdb file for them. Now, opening the full pdb and the
xe.pdb, these latter can also be seen at their full VDW size, at - of
course - their expected position. For me it is still puzzling why so,
although it has solved my problem.

I used linux 32bit 1.4.1, 30282 build (the last one)


On Thu, Mar 25, 2010 at 5:50 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> If you want to see the full VDW size of those residues, use the sphere
> representation.
> 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
> -----
> 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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