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Hi all,
I am trying to model an alternate conformation in my structure, but the alternate conformation is a completely different residue. For example, if two different ligands bound in the same position just at shared occupancies.  I saw an old posting about this same issue and they recommended giving different segids to different ligands and omitting their interactions, and referred to this paper: Liu et al, biochemistry 2005, 44(8):2982-92.

I did this bu I am unable to get CNS to view them as alternate conformations, and during refinement it views them as steric clashes. My question is how/where/in what file do you omit the interactions? Do you modify the .mtf file or some input file?

Thanks!
Krystle