VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Feb 19 2019 - 13:37:20 CST

Hi Matthieu,

VMD 1.9.3 quietly introduced a "mol volmove" command with the following syntax.

mol volmove <molid> <matrix> [<volID>]

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
1300 Morris Park Ave, Bronx, NY 10461
Ullmann Building 217
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