[Chimera-users] zone command

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 2 11:32:05 PDT 2009

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.

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.  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:

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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