VMD-L Mailing List

From: Matthieu Benoit (matthieu.benoit76_at_orange.fr)
Date: Tue Feb 19 2019 - 13:04:38 CST

Dear Ryan,

 

Many thanks for the answer and the script. Looking at it and at the DX format, it seems that the DX header modification will account for the translational component of the alignment but not for the rotational one, right? 

The rotations are large in my case since I align subsets of large structures with conformational changes. Is the new command you mention available in one of the test version available on BioCoRE?

 

Thanks,

 

Matthieu

 

> Message du 19/02/19 19:33
> De : "Ryan McGreevy"
> A : "Matthieu Benoit"
> Copie à : vmd-l_at_ks.uiuc.edu
> Objet : Re: vmd-l: Move volumetric data with their associated PDB
>
>

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 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

>  

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> Matthieu BENOIT
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