How can I invert the configuration of a pdb file to create the mirror image model of the protein molecule? Thanks, Steve Kent Stephen Kent Professor of Chemistry Professor of Biochemistry & Molecular Biology Institute for Biophysical Dynamics Mail: Gordon Center for Integrative Science, Room W204 University of Chicago 929 East 57th Street Chicago, IL 60637, USA Tel: +1 773 702 4912 Email: skent@uchicago.edu
Hi Steve, Chimera doesn't include anything to do this, sorry. I believe you would just need a script to reverse the signs of all x, or all y, or all z atomic coordinates depending on the desired plane of reflection. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 30, 2010, at 2:15 PM, Stephen B.H. Kent wrote:
How can I invert the configuration of a pdb file to create the mirror image model of the protein molecule? Thanks, Steve Kent
Stephen Kent Professor of Chemistry Professor of Biochemistry & Molecular Biology Institute for Biophysical Dynamics
On Jan 3, 2011, at 11:21 AM, Elaine Meng wrote:
Hi Steve, Chimera doesn't include anything to do this, sorry. I believe you would just need a script to reverse the signs of all x, or all y, or all z atomic coordinates depending on the desired plane of reflection.
On Dec 30, 2010, at 2:15 PM, Stephen B.H. Kent wrote:
How can I invert the configuration of a pdb file to create the mirror image model of the protein molecule?
Yes, you could write a Python script, or if you are just doing this once, type this into the IDLE interpreter (under General Controls): m = chimera.openModels.list()[0] for a in m.atoms: crd = a.coord() crd.x = 0 - crd.x a.setCoord(crd) The above assumes that the model you want to invert is the only one open, and inverts it in x (i.e. across the yz plane). Changing the script to invert in y or z is obviously trivial. Hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
I should have noted that if you do this as a script you also need this line at the top: import chimera --Eric On Jan 3, 2011, at 11:26 AM, Eric Pettersen wrote:
Yes, you could write a Python script, or if you are just doing this once, type this into the IDLE interpreter (under General Controls):
m = chimera.openModels.list()[0] for a in m.atoms: crd = a.coord() crd.x = 0 - crd.x a.setCoord(crd)
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Elaine Meng -
Eric Pettersen -
Stephen B.H. Kent