[Biopython] How to apply symmetry matrix on protein chains

[Fred Ludlow]

This doesn't exactly answer your question, but you can get them via FTP,
e.g:
ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/divided/hr/1hri.pdb1.gz

This file contains 60 models (one for each of the BIOMTX matrices in the
original PDB file). Helpfully, biopython knows how to handle multiple
models, so just download, unzip and read that in
http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec162


Fred


ps. If you want to understand how it works, or write your own code to do it:

You use the BIOMT records to create a series of 3x3 matrices. e.g. these
three lines from the PDB file correspond to one transformation:

REMARK 350   BIOMT1   2  0.500000 -0.809017  0.309017        0.00000

REMARK 350   BIOMT2   2  0.809017  0.309017 -0.500000        0.00000

REMARK 350   BIOMT3   2  0.309017  0.500000  0.809017        0.00000

use these to make a matrix

>>> import numpy as np
>>> m = np.array([[ 0.5,      -0.809017,  0.309017],
              [ 0.809017,  0.30917,  -0.5     ],
              [ 0.309017,  0.5,       0.809017]])

Then for each coordinate in your original PDB, e.g. the first one:
>>> a = np.array([35.887,  31.402,  96.395])

take the dot product:
>>> np.dot(m,a)
array([  22.32644188,   -9.45575058,  104.77588679])

You'll see these coordinates correspond to the first line of model 2 in the
biological assembly file I linked above (line 6480)



On 13 November 2014 06:50, Bhushan <nagbiotech1 at gmail.com> wrote:

> Hi,
>
> I want to apply the symmetry matrix on pdb 1HRI and output the biological
> assembly (with rotated coordinates). Can anyone suggest me a way to do this
> using biopython.
>
> Thank you for your time. I would appreciate any kind of help.
>
>
> With Regards,
> Bhushan.
>
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