[Chimera-users] zones and residue name/number

[Eric Pettersen]

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 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
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
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