Elaine: select :wat & #1 z<1.5 delete sel followed by select :popc & #1 z<1.5 delete sel work. That is, residue WAT is indeed in the membrane file, though it is not seen there by the command select #0 & #1 z<1.5 It is seen as solvent. In fact, as I told some emails ago, the Taskbar command Select Structure Solvent allowed to remove all WATs. On reading what you suggested, my understanding is that those three records for water are seen as solvent no matter how the residue is named. So that my scrambling of names failed to perform. Thanks francesco --- 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. 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
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