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Re: PROTIN and alternate conformations



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Stefano Trapani wrote:
> 
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> 
> I am refining (PROTIN/REFMAC) a structure which includes a cysteine with two
> alternate side chain conformations (A and B):
> 
> ATOM   1707  CA  CYS   219       1.641  -3.093  30.775  1.00 21.13   6  C    C
> ATOM   1708  C   CYS   219       2.624  -2.584  29.732  1.00 19.58   6  C    C
> ATOM   1709  O   CYS   219       3.835  -2.550  30.008  1.00 18.97   8  C    O
> ATOM   1710  CB ACYS   219       0.765  -1.947  31.289  0.50 22.99   6  C    C
> ATOM   1711  SG ACYS   219      -0.794  -2.403  32.095  0.50 27.22  16  C    S
> ATOM   1712  CB BCYS   219       0.616  -2.047  31.146  0.50 23.71   6  C    C
> ATOM   1713  SG BCYS   219       1.054  -1.000  32.528  0.50 28.57  16  C    S
> 
> It seems that the A conformer is making a disulphide bond with the B
> conformer of the same residue from a symmetry related (-Y,X-Y,Z) chain.
> 
> How can I specify a PROTIN special distance restraint between the
> sulphur atoms of the A conformer and the symmetry related B conformer?
> 


 If there is a special problem, you can be sure one of the insulin
structures will have displayed it! This is really difficult; you can use
this sort of format:

SPEC CHNNAM J D ATNA ZN ND1 RESN 4 9 DIST 2.1 1 1 SYMM Y-X,-X,Z


 But the special checks dont like two atoms from the same residue with
the same stem and it would mean a major rewrite for PROTIN..

 Maybe the easiest way is to give the B conformation a different CHAIN
ID; 
( It makes life awfully difficult not to have a CHAIN ID; just add one
with PDBSET
pdbset xyzin my-cds.pdb xyzout newcds.pdb
CHAIN A
END

Then you can put the secon conformation in as CHAINID Z

Like this:
ATOM   1707  CA  CYS A 219       1.641  -3.093  30.775  1.00 21.13   6 
C    C  
ATOM   1708  C   CYS A 219       2.624  -2.584  29.732  1.00 19.58   6 
C    C  
ATOM   1709  O   CYS A 219       3.835  -2.550  30.008  1.00 18.97   8 
C    O  
ATOM   1710  CB ACYS A 219       0.765  -1.947  31.289  0.50 22.99   6 
C    C  
ATOM   1711  SG ACYS A 219      -0.794  -2.403  32.095  0.50 27.22  16 
C    S  
ATOM   1712  CB BCYS Z 219       0.616  -2.047  31.146  0.50 23.71   6 
C    C  
ATOM   1713  SG BCYS Z 219       1.054  -1.000  32.528  0.50 28.57  16 
C    S  

 ( Dont forget to define a CHNTYP 1 CHNID Z)
CHNNAME ID A CHNTYP 1
CHNNAME ID X CHNTYP 1
.....
SPEC CHNTYP A C RESN 219 219 ATNA 'SG A' 'SG B' DIST 2.0 1 3 SYMM Y,X,-Z
  to include the di-sulphide..

Then you have to build all the peptide link by hand:
SPEC CHNTYP A C RESN 219 219 ATNA  CA    'CB B' DIST 1.530 1 1 
SPEC CHNTYP A C RESN 219 219 ATNA  C     'CB B' DIST 2.504 2 2
SPEC CHNTYP A C RESN 219 219 ATNA  N     'CB B' DIST 2.455 2 2
SPEC CHNTYP A C RESN 219 219 ATNA  CA    'SG B' DIST 2.810 1 3 


OK?

 Eleanor Dodson