VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Mar 20 2018 - 10:00:57 CDT

Your transformation matrix was calculated for a certain angle of rotation.
Right? What is that angle?
If the angle was say 180 degrees than 2 rotations will bring the structure
back to its starting point.

What is the structure that you are working with? Is it a protein? something
symmetric?

Are you still trying to do the same thing as before? By before I mean when
you question was originally answered?

On Wed, Mar 21, 2018 at 3:29 AM, Peter Mawanga <
peter.mawanga.lagos_at_gmail.com> wrote:

> Hello VMD users
>
> I want to apply a 4*4 Quaternion Transformation Matrix "M" to a set of PDB
> coordinates to get propagating structures.
>
> Upon applying the matrix M successively to the PDB coordinates, I don't
> get propagating structures. But instead get back to the starting
> coordinates after second successive transformation.
>
> The first transformation works well and gives me a dataset "ds2". However,
> upon applying the transformation matrix M to ds2, I get back to the
> original dataset "ds1", instead of a distinct dataset "ds3".
>
> Is there any way of escaping this? Please check the text and link given
> below:
>
> "Then we consecutively docked to each of the dimers additional copies of
> the centroid (one at a time) with docking rotation and translation
> parameters, as were used in the initial docking complex configuration
> selected by the Hex program, to extend the dimers. This procedure used
> three-dimensional (3D) transformation matrices that were preliminarily
> calculated for each of the starting dimers."
>
> https://content.iospress.com/download/journal-of-
> alzheimers-disease/jad131589?id=journal-of-alzheimers-disease%2Fjad131589
>
>
> Forwarded conversation
> Subject: vmd-l: Writing all transformed coordinates into single file
> ------------------------
>
> From: Peter Mawanga <peter.mawanga.lagos_at_gmail.com>
> Date: Thu, Mar 15, 2018 at 12:53 AM
> To: Vmd l <vmd-l_at_ks.uiuc.edu>
>
>
> Dear VMD users
>
> I am trying to apply a transformation matrix successively to a set of pdb
> coordinates and save the coordinates after each transformation into a
> single pdb file. I have been able to write the coordinates separately to
> multiple files though. My code (attempt) is given below:
>
> set sel [atomselect top all]
> set matrix {<4 * 4 transformation matrix>}
> set n {10}
>
> for {set i 0} {$i < $n} {incr i} {
> animate write pdb $i.pdb
> $sel move $matrix
> $sel update
> }
>
> $sel delete
>
> The "beg <first frame> end <last frame>" could not be applied in this
> case, since only one frame is involved. Kindly let me know your suggestions.
>
> --
> Cheers
> Peter
>
> ----------
> From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> Date: Thu, Mar 15, 2018 at 2:21 AM
> To: Peter Mawanga <peter.mawanga.lagos_at_gmail.com>, Vmd l <
> vmd-l_at_ks.uiuc.edu>
>
>
> Hi Peter,
>
> If I understand this correctly, you start from one molecule loaded with a
> single frame, apply a single transformation matrix n times, and end up with
> n+1 total frames written out to some file. If so, you just need to call
> "animate dup" at the appropriate time, making your script look like this:
>
>
> set sel [atomselect top all]
> set matrix {<4 * 4 transformation matrix>}
> set n {10}
>
> for {set i 1} {$i <= $n} {incr i} {
> animate dup frame [expr {$i-1}] top
> $sel frame $i
> $sel move $matrix
> }
> animate write pdb $i.pdb
> $sel delete
>
>
> The other (slower) alternative is to load your initial pdb multiple times
> until you have as many frames as you need, and then apply your
> transformation successively.
>
> -Josh
>
> ----------
> From: Peter Mawanga <peter.mawanga.lagos_at_gmail.com>
> Date: Thu, Mar 15, 2018 at 6:05 PM
> To: "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
> Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
>
>
> Hello Josh
>
> Thanks a lot! Yes what you have written is the case. I had never used
> "dup" before. The above command works except:
>
> animate dup frame [expr {$i-1}] top
>
> Needs to be replaced with:
>
> animate dup frame [expr {$i-1}] <molID>
>
> I then replaced all the "END" keywords in the output PDB file with "TER";
> as I want to view all of the transformations together.
>
> --
> Cheers
> Peter
>
>
>
>
> --
> Cheers
> Peter
> 

-- 
Best,
/A