Hi Kanika,
First of all, please try to phrase your questions in fully written english,
in stead of a phonetic-like writing with lots of abbreviations... It's
sometimes kind of hard to follow. The reason for it, as well as other very
useful hints are expanded on
http://www.catb.org/~esr/faqs/smart-questions.html which is a very good read
:)
As for the question, it may well be that the crystal structure does not give
an indication for the existence of a multimer, whereas an empirical method
may predict multimers.
For predicting multimers, Hongbo Zhu previously suggested the following
site:
http://pdbwiki.org/index.php/Biological_unit
at the bottom of the page you can find four very useful servers for the
determination of biological units of proteins (PQS is not updated anymore):
The Protein Quaternary Structure Server (PQS) [2] or [3]
The Macro-Molecular Structure Database (MSD) [4] or [5]
The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
Protein quaternary structure investigation (PiQSi) [7]
Please try them and see if they help you obtaining what you need.
For a given BIOMT record in a PDB file, like:
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 75.42600
REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 75.42600
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -33.90600
You should read them as:
REMARK 350 BIOMT1 1 R1xx R1xy R1xz t1x
REMARK 350 BIOMT2 1 R1yx R1yy R1yz t1y
REMARK 350 BIOMT3 1 R1zx R1zy R1zz t1z
REMARK 350 BIOMT1 2 R2xx R2xy R2xz t2x
REMARK 350 BIOMT2 2 R2yx R2yy R2yz t2y
REMARK 350 BIOMT3 2 R2zx R2zy R2zz t2z
Where R is a rotation matrix and t a translation vector to be applied after
rotation. For any coordinate u=(x1 y1 z1) you then get the corresponding
v=(x2 y2 z2) from v = Ru + t. This means that in your case x2 = R2xx*x1 +
R2xy*y1 + R2xz*z1 + t2x. And similarly for the other coordinates. You can
figure out how then to construct the line for alter_state.
But hadn't you already bin pointed to this page and the script there?:
http://www.pymolwiki.org/index.php/BiologicalUnit
Hope it helps,
Tsjerk
On Wed, Mar 9, 2011 at 8:43 AM, kanika sharma <ksharma...@gmail.com> wrote:
>
> 1BX7...the author determined structure is monomeric..PISA generate dimeric
> assembly
>
> REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
> REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
>
>
> *Remark 350 in orthogonal coordinates*
>
> REMARK 350
> REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
> REMARK 350 SOFTWARE USED: PISA 1.18
> REMARK 350 TOTAL BURIED SURFACE AREA FOR THE COMPLEX: 2330 A**2
> REMARK 350 SURFACE AREA FOR THE COMPLEX: 6730 A**2
> REMARK 350 GAIN IN SOLVENT FREE ENERGY: -49 KCAL/MOL
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
> REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
> REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 75.42600
> REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 75.42600
> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -33.90600
>
>
>
> can sm1 tell howz it???is it dat in crystal study no dimeric formis seen???
>
> and wt cud b the code for this BIOMT transformations...
>
>
>
> Regards,
> Kanika
>
>
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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