VMD-L Mailing List

From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Fri Mar 13 2020 - 17:00:55 CDT

Ok, thanks for the clarification. So visualization state cannot be used to
transform the actual positions then.

On Fri, Mar 13, 2020 at 10:49 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> Nope. Visualization states only save camera positions, probably to reduce
> the file size. In these cases, I just save the moved coordinates to a new
> file, and create a new visualization states after loading the repositioned
> file.
> Josh
>
> On Fri, Mar 13, 2020, 5:43 PM Peter Mawanga <peter.mawanga.lagos_at_gmail.com>
> wrote:
>
>> 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
>>
> 

-- 
Cheers
Peter