VMD-L Mailing List

From: Faisal, H M Nasrullah (hmnasrullah.faisal_at_ndsu.edu)
Date: Tue Oct 06 2020 - 22:07:28 CDT

Hi John,

Thanks for your kind response. But I cannot upload .map file in vmd. Whenever I try, it gives me the following error message.
Unable to load molecule.
I am using VMD 1.9.3. Can you please give me some insight?

Thanks
Faisal

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Tuesday, October 6, 2020 8:57 PM
To: Faisal, H M Nasrullah <hmnasrullah.faisal_at_ndsu.edu>
Cc: VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Converting electron density data from .map to .dx in vmd

Hi,
  You didn't provide any error messages, but I'm guessing that voltool
code didn't recognize the file extension of your ".map" file.
Several map formats claim ".map" as their extension so in such a case its best
to manually disambiguate for VMD by loading it into a new molecule
and using, e.g., "voltool write -mol 0 -vol 0 -o file.dx" to write it out.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 30, 2020 at 04:16:29PM +0000, Faisal, H M Nasrullah wrote:
> Hi all,
> I am trying to perform some MDFF calculations. I have downloaded the
> electron density data from [1]https://www.emdataresource.org/ in .map
> format. Then I have tried to convert it in .dx format in vmd using the
> command:
> voltool write -i density.map -o density.dx
> But it didn't work. How can I convert a .map file download from
> EMDataResource into .dx file in VMD?
> Thanks in advance.
> Faisal
>
> References
>
> Visible links
> 1. https://www.emdataresource.org/ 

--
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/