[Chimera-users] Aligning a protein into a membrane

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 21 10:36:04 PST 2007

Hi Francesco,
You can always view the chimera-users archives to see old messages,

Here is the message describing how you can remove the overlapping  
molecules BEFORE you write the PDB file from Chimera

and the one that mentioned writing PDB

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).

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

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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