[Chimera-users] Aligning a protein into a membrane

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 22 08:46:43 PST 2007

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  
> 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"

and this is the User's Guide page (see especially the parts about zones  
and combinations):

> 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.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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