[Chimera-users] Aligning a protein into a membrane

[Francesco Pietra]

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 at 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 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
> 
> 
> 



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