VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Feb 19 2019 - 13:17:05 CST

There have been a couple versions of that script (which is one reason it
has now been simplified and incorporated into VMD properly), but I think
that script should do both translation and rotation. However, it does look
like the latest 1.9.4 alpha release (a27)
https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
has the new built in command if you want to try that. It is in the new
`voltool` command which contains many volumetric data manipulation routines
(and replaces the old volutil plugin). The command you want is `voltool
move` which takes a 4x4 matrix just like you get from `measure fit` and
applies it to a specified map. No need to convert any files or modify any
headers.

On Tue, Feb 19, 2019 at 2:05 PM Matthieu Benoit <matthieu.benoit76_at_orange.fr>
wrote:

> 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" <ryanmcgreevy_at_ks.uiuc.edu>
> > A : "Matthieu Benoit" <matthieu.benoit76_at_orange.fr>
> > 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 <
> 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
>> > **************************************************
>> >
>> >
>>
>