VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Feb 19 2019 - 12:33:06 CST

In the upcoming release of VMD there will be a new command to do this much
more easily, but for now you can use this script:
http://www.ks.uiuc.edu/Research/mdff/scripts/move_dx.tcl
As you guessed, it uses the matrix from `measure fit` between the two
structures. You will have to convert the map you want to move to .dx format
first, so you can modify the header information. To do this, you can use
the command `volutil mymap.mrc -o mymap.dx' in the TkConsole of VMD. The
top of the .dx file will have a header with the information you need to
supply to the script. You will also then change the header to what the
script gives you as output.

On Tue, Feb 19, 2019 at 1:22 PM Matthieu Benoit <matthieu.benoit76_at_orange.fr>
wrote:

> Hi,
>
>
>
> I have 2 similar PDB structures (molid 0 and 1) with their associated
> cryo-EM map in MRC format.
>
> I've loaded each map in its corresponding molecule (molid 0 and 1
> respectively) with "mol addfile".
>
> I've then aligned the atom positions of mol 0 on mol 1 with 'measure fit'
> and 'move'.
>
> The volume of mol 0 does not move however. I would like that it's relative
> position to the atoms of mol 0 stay the same (so that it gets aligned too).
>
> What should I do to achieve this? I guess I'll have to use the matrix from
> 'measure fit' and apply it to the volumetric data but I don't know how the
> volumetric data is represented in VMD.
>
>
>
> Thanks for any advice,
>
>
>
> Matthieu
>
>
>
> **************************************************
> Matthieu BENOIT
> Albert Einstein college of medicine
> 1300 Morris Park Ave, Bronx, NY 10461
> Ullmann Building 217
> **************************************************
>
>