Thank you all for the replies. 


 Analysis of protein interfaces suggests that the following  quaternary structures are stable in solution (I wonder the DGdiss is positive value, is it significant to make Hexamer assembly because I couldnt find any help to find out about the allowed values)

 ----.-----.---------------------------------------.---------------
 Set |  No | Size  Id      ASA       BSA    DGdiss | Formula
 ----+-----+---------------------------------------+---------------
   1 |   1 |   6    0   19917.7    5536.3      3.8 |     A(2)B(2)C(2)
 ----+-----+---------------------------------------+---------------
   2 |   2 |   3    1   10722.9    2004.1      6.2 |      ABC
 ----+-----+---------------------------------------+---------------
   3 |   3 |   4    2   14004.2    3014.9      0.5 |      A(2)B(2)
     |   4 |   1    3    4217.5       0.0         -0.0 |      A
 ----+-----+---------------------------------------+---------------
   4 |   5 |   2    4    7506.2    1003.3      7.0 |        AB
     |   6 |   1    3    4217.5       0.0        -0.0 |        A
 ----+-----+---------------------------------------+---------------
   5 |   7 |   2    5    7443.8    1000.8      6.8 |      AB
     |   8 |   1    6    4282.4       0.0     -0.0 |         A
 ----+-----+---------------------------------------+---------------
   6 |   9 |   2    7    7556.5    1008.3      2.0 |      A(2)
     |  10 |   1    8    4227.1       0.0     -0.0 |        A
     |  11 |   1    3    4217.5       0.0     -0.0 |        A
 ----'-----'---------------------------------------'---------------


Waiting for your reply 

Thanks 


H




On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick <robert.fenwick@irbbarcelona.org> wrote:
Also, if you would like to try homology modelling then that could work. However you would need a couple of hexamer strucutres to start with. It would probably take some tinkering with current tools. I would probably use an MD approach to solve this problem. 

Sorry I don't have a quick fix this is not my current area of expertise. 

Bryn

Sent from my iPod

On 19/05/2010, at 09:22, humayun scherrif <hum.one@gmail.com> wrote:


Thank you Bryn for your reply, But I have already tried all possible symmetries that it generates, but it does not provide a proper hexameric assembly. Does it mean this is due to problems in crystal packing ? 

Is there any alternative way to generate or by homology, which server could be suitable ? 


Regards

H


On Wed, May 19, 2010 at 4:02 PM, Robert Brynmor Fenwick <robert.fenwick@irbbarcelona.org> wrote:
There is a symmetry command that will build the crystal symmetry from
the pdb header you could then delete the irrelevent molecules to leave
the six that you want.

Bryn

If you have trouble with this I can hunt down the commands in my labbook


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