Quoting Andrew Purkiss-Trew <[email protected]>:
Quoting "Critton, David" <[email protected]>:
Dear CCP4BB,
I am building a protein structure containing a pair of cysteines
linked via disulfide bond. This disulfide bond (i.e. the cysteine
S-gamma atoms) refines well at 2/3 occupancy, however the electron
density suggests that these cysteines each adopt a second, unlinked
conformation (presumably at 1/3 occupancy). I have no trouble
building the alternate conformers; however, refinement causes both
conformers to disulfide-bond.
I would like to know if there is a way (and how) to specify
individual conformers (or individual atoms) in the SSBOND record of
a PDB.
Having seen Garib's response, the SSBOND record was probably a LINK
when I was refining the structure. I will check tomorrow if this was
the case.
In a structure I refined a few years back, I had a similar
situation, with Cys 18 partially disulphide bonded to Cys 22 in one
chain (of two). In the case, the whole loop (plus one residue either
side) between the CYS was modelled with two conformations. The
structure was refined with Refmac version 5.2.0019 and the pdb code
is 2V2U, if you are interested.
From this file, the SS Bond record is
SSBOND 1 CYS A 18 CYS A 22 1555
1555 2.05
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