Well, with the new "smart" display, Chimera will hide atoms that it doesn't think are "interesting". Perhaps the Xenon atoms are being considered uninteresting, in which case you would need to display them explicitly, i.e. "disp Xe", or Select->Chemistry->element->other->Te- Zr->Xe followed by Actions->Atoms/Bonds->show. --Eric On Mar 29, 2010, at 7:25 AM, Francesco Pietra wrote:

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)

Thanks francesco

On Thu, Mar 25, 2010 at 5:50 PM, Elaine Meng <meng@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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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