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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