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
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: <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
On Fri, Oct 2, 2009 at 8:32 PM, Elaine Meng <meng@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 today. I have no more looked at the "segmentation fault" on i386; I am using 64bit chimera also because of huge files. Thanks francesco
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
participants (2)
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Elaine Meng -
Francesco Pietra