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@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