[Chimera-users] Aligning a protein into a membrane

[Elaine Meng]

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 at 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