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 <ksharma997@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