VMD-L Mailing List
From: Karol KASZUBA (karol.kaszuba_at_ist.ac.at)
Date: Sat Mar 04 2017 - 05:49:53 CST
Thanks for both of you!
From: Steven Cohen [secohen_at_mit.edu]
Sent: Friday, March 03, 2017 5:49 PM
To: Karol KASZUBA
Subject: Re: vmd-l: convert .mrc map to .dx format
So far as I know MDFF requires a .situs format EM map. You can convert map formats using several programs. I use e2proc3d.py, which is part of EMAN 2. Depending on the file you convert you may need to define certain variables, such as the pixel size or origin. For example, to convert an .hdf file to .situs, I need to define the pixel size as such
e2proc3d.py foo.hdf foo.situs --apix=#.##
I want to fit my structure into EM map.
I have an initial.pdb and density into which it needs to be fitted, but there is a problem: in order to generate MDFF potential I need a map in .dx format. So, I need to convert from .mrc to .dx.
I tried to google it out, but I can't find nothing about it.
-- Steven Cohen Graduate Student, Drennan Lab Department of Chemistry Massachusetts Institute of Technology secohen_at_mit.edu<mailto:secohen_at_mit.edu>