VMD-L Mailing List

From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Fri Mar 13 2020 - 16:43:38 CDT

Hello Josh

Thanks a lot for the reply. I moved two molecules using the "Mouse > Move >
Molecule" option and wanted to save the new coordinates. However, I was
unable to do so, although I could save the changes as a visualization
state.

>From what I understand, the visualization state doesn't represent the
actual coordinates of the different molecules. Is there any way to save the
positions of the molecules as observed in the visualization state? Please
let me know if feasible.

On Fri, Mar 13, 2020 at 9:06 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> Hi Peter,
>
> I'm not sure what you are trying to do, but those matrices should change
> the position of the camera, not the coordinates stored in VMD. I believe
> that the matricies within viewpoints are meant to be applied to the
> center_matrix, rotate_matrix, and scale_matrix accessible through molinfo
> (see https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node142.html).
> Have you tried something like (operating from memory):
>
> molinfo top set center_matrix {{1 0 0 -119.535} {0 1 0 -144.59} {0 0 1
> -132.454} {0 0 0 1}}
> molinfo top set rotate_matrix {{-0.409795 -0.495426 0.765888 0} {0.679365
> 0.394516 0.618708 0} {-0.608684 0.773872 0.174909 0} {0 0 0 1}}
> molinfo top set scale_matrix {{0.0305694 0 0 0} {0 0.0305694 0 0} {0 0
> 0.0305694 0} {0 0 0 1}}
>
> That is what the saved state uses to re-establish the camera positions.
>
> -Josh
>
> On Fri, Mar 13, 2020 at 12:32 PM Peter Mawanga <
> peter.mawanga.lagos_at_gmail.com> wrote:
>
>> Hello everyone
>>
>> From the visualization state, I got the following matrix for changing the
>> position of a molecule.
>>
>> set viewpoints([molinfo top]) {{{1 0 0 -119.535} {0 1 0 -144.59} {0 0 1
>> -132.454} {0 0 0 1}} {{-0.409795 -0.495426 0.765888 0} {0.679365 0.394516
>> 0.618708 0} {-0.608684 0.773872 0.174909 0} {0 0 0 1}} {{0.0305694 0 0 0}
>> {0 0.0305694 0 0} {0 0 0.0305694 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1
>> 0} {0 0 0 1}}}
>>
>> However, after applying the three matrices successively (since the fourth
>> matrix is redundant and doesn't make any difference anyway after
>> application), all the coordinates were reduced to almost insignificant
>> decimal values.
>>
>> I tried using the "Save coordinates" option to save the molecule position
>> after loading the visualization state but it didn't make any difference.
>> The "measure fit" command returned an identity matrix too.
>>
>> Please suggest how to proceed with this issue.
>>
>> --
>> Thanks
>> Peter
>>
> 

-- 
Cheers
Peter