--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
On Nov 22, 2007, at 3:08 AM, Francesco Pietra wrote:
I tried a lot of different combinations, without picking the right one, in order to remove water from only the zone from where POPC molecules are removed. I changed selections in Taskbar .. Select ... Zone, as if they were reflected to the command-line command or not. In all cases, it was only the command command-line command
select #0 & #1 z<1.5
that worked. Of course, select solvent .. delete did not work, all WAT residues were removed. That is, I don't understand is how "select" of command "select #0 & #1 z<1.5" operates, i.e. why it only recognizes POP residues and not WAT residues in the membrane pdb. I tried to remove TER records, and even renaming WAT: in any case, only POPC were removed.
Hi Francesco, The example command above means: select atoms that are (1) in model 0 AND (2) that are in residues with any atom within 1.5 angstroms of model 1. Perhaps your POPC molecules are in model 0 and your water molecules are not.
As I wrote, the plugin furnishes the membrane with the lipid molecules hydrated at the polar head. The pdb (all atoms ATOM) is a series of POPC residues alternated with series of WAT residues (as I renamed them, because they call them TIP3). I even exchanged the names, calling POP the water residues and WAT the lipid residues: still the water in the area freed from the lipid. This is why I asked what is "select" addressing.
Hopefully your protein is model 1.
Absolutely it is.
You could try ":wat" instead of "#0" but I recommend spending a little time to understand command-line atom specification, which will allow to you generalize to your different situations. There are some examples on the second page of the PDF "quick reference" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf
and this is the User's Guide page (see especially the parts about zones and combinations): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html
I'll try also all that. I am replying just to assure you that - although naive and primitive - before asking for help I am reflecting.
All atoms, for both POPC molecules and water molecules, are called ATOM. This was done by the plugin. (if this matters). Thanks francesco
I am not sure what you mean by "plugin" (VMD plugin?)
Yes, VMD, the only one I am aware of.
but I believe they are supposed to be HETATM in the file written out by Chimera.
Yes, they are renamed HETATM by Chimera.
Maybe they are only HETATM when combined with the protein in a single file. Either way, it may still be necessary for you to edit the file depending on what AMBER needs, sorry.
Having to use more than one "house" in this case, I am becoming more patient than usual. Luckily, it is easy to write Python scripts for modifying the files. I came to Python just for that and it was an extraordinary encounter. Thanks francesco
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
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