[Chimera-users] zone command

Francesco Pietra chiendarret at gmail.com
Fri Oct 2 11:08:46 PDT 2009


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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