## VMD-L Mailing List

**From:** Peter Mawanga (*peter.mawanga.lagos_at_gmail.com*)

**Date:** Tue Mar 20 2018 - 09:29:06 CDT

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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."

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

**Next message:**Brian Radak: "Re: Adding Hydroxide Ions to the simulation box"**Previous message:**Aman Jindal: "Adding Hydroxide Ions to the simulation box"**Next in thread:**Ashar Malik: "Re: Propagating PDB coordinates using Quaternion matrix"**Reply:**Ashar Malik: "Re: Propagating PDB coordinates using Quaternion matrix"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]