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igroup question

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  • Nic Steussy
    All, 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
    Message 1 of 1 , Apr 13, 2005
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      All,

      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
      clue.

      Thanks in advance.

      Nic out

      P.S. Recent spectacular script. The CoA is segid D and the HMG segid E.

      igroup
      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
      end


      --
      -------------------------
      C. Nicklaus Steussy, M.D., Ph.D.
      Purdue University
      csteussy@...
      ------------------------
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