From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Fri Mar 30 2018 - 12:51:59 CDT

Hello Ashar and Joshua

My sincere apologies for the delayed response and not understanding the way
the transformation matrix works. The matrix is totally fine! In the earlier
docking matrix I had posted, the docked structure w.r.t. receptor was just
an inversion and then reflection (or vice-versa) of the original starting
structure (same as receptor).

Hence upon applying the matrix again, it was returning the peptide back to
the receptor 3D position. In short, the structure was not propagating.

As for Joshua's question, the docking matrix now does result in a
pentameric channel if I impose "Random Coil" configuration with "Protein
Builder" in "Molefacture".

Thanks a lot for the valuable inputs and especially cheers to Ashar for
helping me with the script and understanding of the Transformation Matrix
elements.

On Fri, Mar 23, 2018 at 10:54 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Peter,
>
> This wouldn't happen to be a pentameric channel of some kind, would it?
> This is a recording of what I did, and this transformation matrix
> definitely does what it is supposed to.
>
> set M [list [list -8.055069e-01 1.664229e-01 5.687372e-01
> 6.593901e+01 ] [list 2.020147e-01 9.793824e-01 -4.700835e-04
> -1.096723e+01 ] [list -5.570895e-01 1.145146e-01 -8.225191e-01
> -3.810996e+00 ] [list 0.000000e+00 0.000000e+00 0.000000e+00
> 1.000000e+00 ]]
>
> set sellist [list [atomselect top "all" frame 0]]
> set sel [atomselect top "all"]
> for { set f 0 } { $f < 4 } { incr f } {
> animate dup top
> $sel frame [expr {$f+1}]
> $sel move $M
> lappend sellist [atomselect top "all" frame [expr {$f+1}]]
> }
> #Now fuse all the monomers into one structure...
> package require topotools
> set newmol [::TopoTools::selections2mol $sellist]
>
>
> In general, you can't directly decompose a multiplied 4x4 matrix into its
> constituent elements and apply them separately.
>
> -Josh
>
> On 03/21/2018 11:08 AM, Peter Mawanga wrote:
> Hello VMD users
>
> I have a Transformation Matrix:
>
> -8.055069e-01 1.664229e-01 5.687372e-01 6.593901e+01
> 2.020147e-01 9.793824e-01 -4.700835e-04 -1.096723e+01
> -5.570895e-01 1.145146e-01 -8.225191e-01 -3.810996e+00
> 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
>
> And I would like to decompose it into individual rotations and
> translations along XYZ axes. I used this online tool:
> https://www.andre-gaschler.com/rotationconverter/
> /na01.safelinks.protection.outlook.com/?url=https%3A%2F%
> 2Fwww.andre-gaschler.com%2Frotationconverter%2F&data=
> 02%7C01%7CJoshua.Vermaas%40nrel.gov%7C1e4a0d38fd214ffd436b08d58f4e593b%
> 7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636572489025921106&sdata=
> heCg1bIQgX%2BOn7YTiWDRI5TYgysrhXP0qXIvbGhGfZE%3D&reserved=0> and
> converted the 3 x 3 matrix (excluding the 4th row and column) into the
> individual axial rotations.
>
> But upon applying the rotations successively along XYZ axes and then doing
> translation along all the three axes gives me a different final coordinate
> value.
>
> Please check the Tcl script used below:
>
> ===================================================
>
> set sel [atomselect top all]
> set com [measure center $sel]
>
> $sel moveby [vecscale -1.0 $com]
> $sel move [transaxis x 14.7782375]
> $sel move [transaxis y 144.6951609]
> $sel move [transaxis z 4.574389]
> $sel moveby $com
>
> $sel moveby {65.939008 -10.967225 -3.810996}
>
> animate write pdb test.pdb
> $sel delete
>
> ===================================================
>
> Is there any modification required in the script? Please let me know.
>
> --
> Thanks
> Peter
>
>

-- 
Cheers
Peter