alternate conformation of substrate

Martin K. Safo msafo at
Mon Apr 17 10:01:41 EST 2000


I am currently refining a protein-substrate complex at 1.9 Å using CNS
version 0.5.  The substrate is disordered in two positions, the shortest
distance between the two conformers is about 1.3 Å.  The initial refined
electron density map generated without the substrate shows a
well-defined density for the two alternate positions and the two
positions could be fitted easily.  I am refining these substrates
treating them as alternate conformation similarly to alternate protein
side chains.  The problem is after annealing one of the conformer is
pushed away from its density away from the other conformer.  Could
someone with experience show me how to go about refining these
disorederd substrates.   A command file will also be appreciated. Could
you please reply to the e-mail address: msafo at
Thank you very much.

Martin Safo


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