[Chimera-users] Aligning a protein into a membrane

Francesco Pietra chiendarret at yahoo.com
Wed Nov 21 09:24:56 PST 2007

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. 

francesco pietra

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