about alternate conformations

From: Ming
Date: 16 September 2011 15:08

Hi,

I was using Refmac from CCP4 to refine a protein's crystal structure. The methionine has half selenium and half sulfur. I was trying to make alternate conformations and let refmac do the refinement. But it keeps giving me error message as follows:

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.5.0109:  Problem with coordinate file

And here is my modified pdb file.

HETATM  403  N  AMSE A 129      ***           N 
HETATM  404  CA AMSE A 129      ***           C 
HETATM  405  CB AMSE A 129      ***           C 
HETATM  406  CG AMSE A 129      ***           C 
HETATM  407 SE  AMSE A 129      ***          SE 
HETATM  408  CE AMSE A 129      ***           C 
HETATM  409  C  AMSE A 129      ***           C 
HETATM  410  O  AMSE A 129      ***           O 
ATOM    411  N  BMET A 129      ***           N 
ATOM    412  CA BMET A 129      ***           C 
ATOM    413  CB BMET A 129      ***           C 
ATOM    414  CG BMET A 129      ***           C 
ATOM    415  SD BMET A 129      ***           S 
ATOM    416  CE BMET A 129      ***           C 
ATOM    417  C  BMET A 129      ***           C 
ATOM    418  O  BMET A 129      ***           O 

I already confirmed with pdb that this is the right format for this case. But refmac doesn't work with it. I wonder if there is any other changes I should make for refmac?

Thank you,


Ming

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From: Ed Pozharski



Do you have the evidence that your incorporation ration was 50%?

On a practical side, try giving the SeMET a different chain ID.  You can
change it back manually after refinement.  Assuming that the side chain
conformation is the same, you can probably just have the selenium atom
added and hope that due to partial occupancy refmac will not apply any
vdw terms.

--
"Hurry up before we all come back to our senses!"
                          Julian, King of Lemurs

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From: Kevin Jin

I did not make it clear. The protocol we used for protein expression always limit the occ of MSE as 0.75. You may estimate your occ of MSE by ED. You can check PDB for JCSG structures.

 

Cheers,

 

Kevin