I am having difficulty with a refinement. The situation is that I
have good data to 1.8A and have refined the structure down to about
0.19/0.20 rwork/free. It has a ligand in the active site, HMG-CoA.
I'm having trouble refining the ligand, and I think that it is because
the thioester bond between the HMG and the CoA may be broken a portion
of the time. So, I'd like to do two things;
1. Refine the HMG and CoA separately, but turn off the VDW energies
between them so they are not unnecessarily forced apart.
2. It the partial break works out, I'll need to refine HMG-CoA, HMG,
and CoA all in the same space.
The protein is broken into multiple segids, and I have been playing
around with the 'igroup interaction' block of commands. The example
in the FAQ is for a symmetry molecule overlap, which is not exactly my
situation, and Google has not been as much help as usual. I've been
randomly trying things, the most recent was rather spectacular in how
it blew the HMG molecule apart. I was hoping someone could pass me a
Thanks in advance.
P.S. Recent spectacular script. The CoA is segid D and the HMG segid E.
interaction (not (segid E or segid D)) (not (segid E or segid D)) end
interaction (not (segid E or segid D) (segid D or segid E) end
interaction (segid E) (segid D) weights * 1.0 pvdw 0.0 end
C. Nicklaus Steussy, M.D., Ph.D.