VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 06 2020 - 23:52:59 CDT

VMD 1.9.3 doesn't incorporate the "voltool" commands, to use them you
would need to use one of the VMD 1.9.4 test builds.

To load the .map file, you'll have to select the file type
manually in the file load GUI. Is it an MRC / CCP4 map file?

Best regards,
  John Stone

On Wed, Oct 07, 2020 at 03:07:28AM +0000, Faisal, H M Nasrullah wrote:
> 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. [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
> [2]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [3]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. https://www.emdataresource.org/
> 2. http://www.ks.uiuc.edu/~johns/
> 3. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/