[BioPython] Superimposer

[mitlox]

Thank you for you email.  I would like only rotate and translate a pdb 
file that I can see the result in a pdb viewer.

Maybe I do not need the Superimposer object to rotate and translate a 
pdb file with known rotation matrix and translation vector?

Do you know how could I rotate and translate a pdb file?

Thank you in advance.

Peter wrote:
> On Tue, Mar 24, 2009 at 11:12 AM, mitlox <mitlox at op.pl> wrote:
>   
>> Hello,
>> I read that the Superimposer works only with the two lists of atoms which
>> contain the same amount of atoms.
>>
>> So I decided to use "Combinatorial Extension (CE)". This program returns a
>> rotation matrix and a translation vector.
>>
>> After the execution of CE I took the matrix and vector and tried to use it
>> with Superimposer:
>>     
>
> Why?  Once you know the transformation, why do you need to try and
> recreate it with the superimposer?  Are you just doing this as a check?
>
>   
>> ------------------------------------------------------------------------------
>> import sys
>> import numpy
>> from Bio.PDB import *
>>
>>
>> pdb_fix = "../files/1z9g.pdb"
>> pdb_mov = "../files/1z9g90.pdb"
>> p=PDBParser()
>> s1=p.get_structure("FIXED", pdb_fix)
>> fixed=Selection.unfold_entities(s1, "A")
>>
>> s2=p.get_structure("MOVING", pdb_mov)
>> moving=Selection.unfold_entities(s2, "A")
>>     
>
> You should be loading in the ORGINAL pdb file here, as the moved one
> won't exist yet, and if it did, you'd apply the transformation twice.
>
> Note you should expect slight differences due to floating point
> calculations.  Your input was:
>
> array([[ 0.19411442, -0.85385352,  0.4829635 ],
>        [ 0.94858825,  0.28884873,  0.12940907],
>        [-0.24999979,  0.43301335,  0.86602515]], dtype=float32)
> array([-0.99996603, -2.00002551, -2.99998283], dtype=float32),
>
> The output was:
>
> array([[ 0.19411439,  0.94858827, -0.24999978],
>        [-0.85385353,  0.28884871,  0.43301335],
>        [ 0.4829635 ,  0.12940907,  0.86602514]]),
> array([-0.06473777,  1.91448618,  3.21410633])
>
> The rotation looks transposed (backwards).  The translation does look
> different... however, if you switch this line:
> sup.set_atoms(fixed, moving)
> to:
> sup.set_atoms(moving, fixed)
> then things agree.  I suspect something is flipped in the logic of
> your script regarding the frames of reference.
>
> Also, at the end you do sup.apply(moving), but you have already
> manually moved these atoms, so won't your PDB file have them moved
> twice?
>
> Peter
>
>