[Chimera-users] Aligning a protein into a membrane

Francesco Pietra chiendarret at yahoo.com
Wed Nov 21 13:14:44 PST 2007

Most sorry that you had to repeat. I succeeded now, with still a problem. I.e,
the membrane lipid (POPC) is hydrated at the head (this is how it can be built
with the plugin). Those molecules of water are still in the space cleaned from
lipid molecules, i.e. they superimpose the protein. 

I am not sure if such water should be removed before solvating the system,
adding ions and MD. If it should be removed, is is another command?

Before posting, I have now checked the saved file for the membrane. Probably
there is a more serious problem: all "TER" records inserted between the POPC
residues and between the WAT residues have been removed on saving (using "Save
relative to model"). That will create problems to Amber, unless lack of TER
records is accounted for by the CONECT records added (in the membrane pdb file
from the plugin I had to add all mentioned TER records to have the file
accepted by Amber)


In contrast, the "TER" record between the protein and the single WAT molecule
within the pore was not removed.

--- Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> You can always view the chimera-users archives to see old messages,
> http://www.cgl.ucsf.edu/pipermail/chimera-users/index.html
> Here is the message describing how you can remove the overlapping  
> molecules BEFORE you write the PDB file from Chimera
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ 
> 002010.html
> and the one that mentioned writing PDB
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ 
> 002008.html
> I didn't say much about writing PDB, but to retain the spatial  
> relationship you have generated in Chimera, you must choose the  
> option to "Save relative to model" and save both models relative to  
> the same number (if they are in 0 and 1, either save both relative to  
> 0 or save both relative to 1, it doesn't matter which).
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb
> 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
> On Nov 21, 2007, at 9:24 AM, Francesco Pietra wrote:
> > Elaine:
> > Relating to your instructions of last 19 Nov (I printed your mail,  
> > then
> > unfortunately I deleted it) how to align a protein into a membrane  
> > (for both I
> > have valid pdb and valid Amber parameters) I am probably made  
> > elusive mistakes
> > at the stage of saving new pdbs.
> >
> > I aligned the protein into the membrane, then (with protein  
> > selected and
> > membrane not active) I saved the new pdb, getting two files, "0"  
> > for the
> > membrane and "1" for the protein.
> >
> > In Amber LEaP both these pdb file could be loaded and combined,  
> > however save
> > top/crd failed because something was wrong with the membrane file.  
> > In fact, if
> > the original pdb for the membrane is used, top/crd can be saved,  
> > though the
> > protein is not accurately aligned.
> >
> > Clearly, my plan is to remove superimpositions among molecules for  
> > the "whole"
> > obtained from Amber.
> > Thanks
> > francesco pietra

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