VMD-L Mailing List

From: Karol KASZUBA (karol.kaszuba_at_ist.ac.at)
Date: Sat Mar 04 2017 - 05:49:53 CST

Hey,

Thanks for both of you!

cheers
Karol

________________________________
From: Steven Cohen [secohen_at_mit.edu]
Sent: Friday, March 03, 2017 5:49 PM
To: Karol KASZUBA
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: convert .mrc map to .dx format

Hi Karol,

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=#.##

Best,
Steve

On Fri, Mar 3, 2017 at 10:51 AM, Karol KASZUBA <karol.kaszuba_at_ist.ac.at<mailto:karol.kaszuba_at_ist.ac.at>> wrote:
Hi,

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.

Any ideas?

thanks
karol 

--
Steven Cohen
Graduate Student, Drennan Lab
Department of Chemistry
Massachusetts Institute of Technology
secohen_at_mit.edu<mailto:secohen_at_mit.edu>