[Chimera-users] zone command

Francesco Pietra chiendarret at gmail.com
Fri Oct 2 13:22:28 PDT 2009

On Fri, Oct 2, 2009 at 8:32 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> I don't understand what you are doing.  There is no zone command, only using
> "z" in other commands to specify a zone.

Hi Elaine: sorry for my bad wording.
> In command-line specifications you can include the model number to specify
> only a particular model and not the other, for example "#0:w" for the
> residues named W in model 0 only.

That's the solution. I should have reviewed that part of the help. If
I can invent an excuse, perhaps I was tired from much other work

I have no more looked at the "segmentation fault" on i386; I am using
64bit chimera also because of huge files.


>  If the residue is named WAT, use :wat
> instead of :w or if it is the atom name and not the residue name, use @wat
> Command-line specification, including zones:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> 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 Oct 2, 2009, at 11:08 AM, Francesco Pietra wrote:
>> Hi:
>> I prepared with the zone command a model (#0) of a protein partly
>> immersed into a hydrated lipidic bilayer (cut-and-paste from the two
>> models from the zone command).
>> Now I would like to solvate with water the part of protein which
>> protrudes out of the bilayer.
>> Water is single-point (coarse-grain simulations) indicated in model #0 as
>> ATOM   2724  W   W    2060      45.420   3.750  23.380  1.00  0.00
>>   W
>> and in the pdb file of the water block (model #1) to be added
>> ATOM  27558  W     W  5018      84.320 142.862  11.262  1.00  0.00
>> Once model #0 and model #1 are superimposed, clearly the zone command
>> does not distinguish W from the two models.
>> How could the zone command be made working now? I renamed W to WAT in
>> model #1 but the zone command does not recognizes WAT under such
>> circumstances. Not yet found a way out, which should be simple. Thanks
>> for suggestions.
>> (solvating model #0 with programs from the MD suite also solvates what
>> it should not; this is why I am trying with CHIMERA)
>> francesco pietra

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