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From: Matthieu Benoit (matthieu.benoit76_at_orange.fr)
Date: Tue Feb 19 2019 - 19:23:39 CST

Many thanks for the answers. Both commands do exactly what I was looking for ('voltool move' in VMD 1.9.4a27 and 'mol volmove' in VMD 1.9.3).

Best,

 

Matthieu

 

> Message du 19/02/19 21:39
> De : "Vermaas, Joshua"
> A : "vmd-l_at_ks.uiuc.edu" , "matthieu.benoit76_at_orange.fr"
> Copie à :
> Objet : RE: vmd-l: Move volumetric data with their associated PDB
>
>

Hi Matthieu,
>
> VMD 1.9.3 quietly introduced a "mol volmove" command with the following syntax.
>
> mol volmove []
>
> Save your matrix that you get from measure fit, and you can apply it to your volumetric data.
>
> -Josh
>  

 

> On 2019-02-19 12:31:37-07:00 owner-vmd-l_at_ks.uiuc.edu 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
> Albert Einstein college of medicine
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