Hi all, I was wondering how to quickly back-compute an electron density map from a PDB using phenix from the command line. I'm assuming it's not hard, but I can't find documentation that would lead me to it. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
Hi Scott,
http://www.phenix-online.org/documentation/reference/maps.html
Is this the documentation you are looking for?
Best,
George
On Thu, Jan 29, 2015 at 8:26 AM, Scott Horowitz
Hi all,
I was wondering how to quickly back-compute an electron density map from a PDB using phenix from the command line. I'm assuming it's not hard, but I can't find documentation that would lead me to it.
Thanks, Scott
-- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute
University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Scott,
I was wondering how to quickly back-compute an electron density map from a PDB using phenix from the command line. I'm assuming it's not hard, but I can't find documentation that would lead me to it.
first you get your PDB file: phenix.fetch_pdb 1akg --mtz then compute 2mFo-DFc and residual mFo-DFc maps: phenix.maps 1akg.pdb 1akg.mtz If you want model calculated map phenix.fmodel 1akg.pdb high_resolution=1 this will give your Fourier map of 1A resolution. We don't have a user-exposed tool to calculate exact electron density map from a PDB file. Pavel
participants (3)
-
George Devaniranjan -
Pavel Afonine -
Scott Horowitz