[Chimera-users] Aligning a protein into a membrane

Francesco Pietra chiendarret at yahoo.com
Thu Nov 22 09:22:48 PST 2007

--- 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.

As I wrote, the plugin furnishes the membrane with the lipid molecules hydrated
at the polar head. The pdb (all atoms ATOM) is a series of POPC residues
alternated with series of WAT residues (as I renamed them, because they call
them TIP3). I even exchanged the names, calling POP the water residues and WAT
the lipid residues: still the water in the area freed from the lipid. This is
why I asked what is "select" addressing.

>Hopefully your protein is model 1.

Absolutely it is.

> 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

I'll try also all that. I am replying just to assure you that - although naive
and primitive - before asking for help I am reflecting.

> > 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?)

Yes, VMD, the only one I am aware of.

> but I believe  
> they are supposed to be HETATM in the file written out by Chimera.

Yes, they are renamed HETATM 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.

Having to use more than one "house" in this case, I am becoming more patient
than usual. Luckily, it is easy to write Python scripts for modifying the
files. I came to Python just for that and it was an extraordinary encounter.


> 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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