VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Mar 21 2018 - 13:34:12 CDT

I will have a play with these files and get back to you at some point later
today. Meanwhile I have added some thoughts on your other query. Hopefully
that will give you another angle to look at things (pun intended).

On Mar 22, 2018 06:27, "Peter Mawanga" <peter.mawanga.lagos_at_gmail.com>
wrote:

> Hello Ashar
>
> I think this problem (M^2=I) could be overcome if the rotations and
> translations are done individually? I have posted another query in this
> forum regarding the same. Please have a look as feasible.
>
> On Wed, Mar 21, 2018 at 2:06 PM, Peter Mawanga <
> peter.mawanga.lagos_at_gmail.com> wrote:
>
>> Hello Ashar
>>
>> I was running the tests with "LFcin P-20" peptide. This time I used Hex
>> program instead and docked the peptide to itself (i.e. both ligand and
>> receptor are the same peptide with same conformation).
>>
>> The transformation matrix for ligand (receptor is fixed/stationary):
>>
>> -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
>>
>> This matrix could be obtained from VMD too with "measure fit" command and
>> with backbones of the receptor and ligand selected.
>>
>> I would like to add the next monomer to the complex (after ligand) such
>> that the receptor-ligand docking pattern propagates further, as shown in
>> the paper. Most probably it would form a ring structure, as per the current
>> docking observation.
>>
>> Please find the receptor, ligand and complex PDB coordinate files
>> attached below.
>>
>> On Wed, Mar 21, 2018 at 11:46 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>>
>>> Hi Peter,
>>>
>>> I originally thought of writing a very long reply, but decided that it
>>> would be easier to just ask you if you could give me the structure that you
>>> are working with and how you want to "propagate" it and I will do it for
>>> you and explain how I did it. The process is quite trivial and explaining
>>> it is just going to exchange a lot of emails between us. So if you give me
>>> the structure it will save time.
>>>
>>> Best,
>>> /A
>>>
>>>
>>> On Wed, Mar 21, 2018 at 7:22 AM, Peter Mawanga <
>>> peter.mawanga.lagos_at_gmail.com> wrote:
>>>
>>>> Hello Ashar
>>>>
>>>> After docking the same peptide conformer to itself, the authors of the
>>>> paper tried to add more copies of the conformer using the same (not sure
>>>> about that!) rotational and translation parameters represented by the 3D
>>>> matrix. I am getting the same exact values upon using "measure fit" command
>>>> in VMD. The slight difference after second transformation might be an
>>>> artefact of decimal precision (in my opinion).
>>>>
>>>> My aim was to get propagating amyloid fibrils as mentioned in the
>>>> study. Maybe I am missing some matrix operation in between.
>>>>
>>>> On Tue, Mar 20, 2018 at 10:45 PM, Ashar Malik <asharjm_at_gmail.com>
>>>> wrote:
>>>>
>>>>> So I did a quick test with the matrix you have provided. It turns out
>>>>> that the matrix you have provided is supposed to give the result you are
>>>>> getting.
>>>>>
>>>>> So the first time you multiply it, it will generate a transformation
>>>>> ds1 and the second time it will take you back to the parent structure
>>>>> (almost). It doesn't recover the exact structure but it is quite close.
>>>>>
>>>>> It is very likely that the program that generated this transformation
>>>>> matrix did this on purpose (or it just happened by chance???) so the
>>>>> operation would become order free (this is my thought and might be
>>>>> completely wrong). Meaning it didn't matter which structure you applied the
>>>>> matrix to, you would get the other structure. So e.g. if you had applied it
>>>>> to the initial conformation you obtain the final one and applying it to the
>>>>> final would return the initial.
>>>>>
>>>>> If you want the parent structure to undergo a certain transformation
>>>>> and for all subsequent iterations to be replicas of that - you should
>>>>> perhaps compute the transformation that does that (which the current one
>>>>> doesn't).
>>>>>
>>>>> However, I think that is not what you want to do. Having a quick skim
>>>>> of the paper attached, they applied the transformation to a structure just
>>>>> once. It appears (i think) that they used different conformers 1 selected
>>>>> from each of the clusters and applied the transformation once so that it
>>>>> comes to a position next to the dimer (i think).
>>>>>
>>>>> You however are applying the same transformation twice? Why?
>>>>>
>>>>> On Wed, Mar 21, 2018 at 4:17 AM, Peter Mawanga <
>>>>> peter.mawanga.lagos_at_gmail.com> wrote:
>>>>>
>>>>>> Hello Ashar
>>>>>>
>>>>>> Thanks for the quick revert. I am first doing rotation along three
>>>>>> Euler angles (denoted by 3 x 3 matrix excluding the 4th row and column) and
>>>>>> then applying the translation along xyz axes (4th column entries). Please
>>>>>> find the matrix below.
>>>>>>
>>>>>> -8.260116e-01 -3.044969e-01 -4.743274e-01 5.280182e+01
>>>>>> -3.042386e-01 -4.675523e-01 8.299601e-01 8.201990e+00
>>>>>> -4.744932e-01 8.298653e-01 2.935639e-01 1.421723e+01
>>>>>> 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
>>>>>>
>>>>>> The structure is a small peptide (20 residues long) used as a test. I
>>>>>> got the transformation matrix by comparing the initial and final
>>>>>> coordinates obtained from a docking server.
>>>>>>
>>>>>> Yes, I am still trying to perform the same operation i.e. do multiple
>>>>>> transformations. I have attached a representative image below that denotes
>>>>>> my objective.
>>>>>>
>>>>>>
>>>>>> On Tue, Mar 20, 2018 at 8:30 PM, Ashar Malik <asharjm_at_gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Cheers
>>>>>> Peter
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Best,
>>>>> /A
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Cheers
>>>> Peter
>>>>
>>>
>>>
>>>
>>> --
>>> Best,
>>> /A
>>>
>>
>>
>>
>> --
>> Cheers
>> Peter
>>
>
>
>
> --
> Cheers
> Peter
>