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. Hopefully your protein is model 1. 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
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?) but I believe they are supposed to be HETATM in the file written out 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. 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