local refinement of target weights?
Hello, I am wondering if there is a way to restrain geometry target weights for a ligand seperate from the rest of the molecule. I would like to impose higher restraints for the ligand than that of the protein in the same refinement run. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Hi Yarrow,
I am wondering if there is a way to restrain geometry target weights for a ligand seperate from the rest of the molecule. I would like to impose higher restraints for the ligand than that of the protein in the same refinement run. Thanks for your help.
currently you can only do it by editing the corresponding esds in ligand CIF file. By making the esds smaller you will make the corresponding restraints stronger. But in general it is dangerous to do, and normally is not recommended. If you make the esds too small, that means the corresponding contribution to overall restraints target arising from that ligand will be overwhelmingly large, so the restraints from other atoms will be negligibly small. In practice this means you will get a model with distorted geometry. This is exactly why often the CIF files created by PRODRG do not work well with phenix.refine (since it sometimes puts very small esds, which explodes refinement). Pavel
Thanks Pavel I hadn't considered the issues you brought up. I have heard of people doing this with CNS but I am not sure how it is done or how well it worked. -Yarrow
Hi Yarrow,
I am wondering if there is a way to restrain geometry target weights for a ligand seperate from the rest of the molecule. I would like to impose higher restraints for the ligand than that of the protein in the same refinement run. Thanks for your help.
currently you can only do it by editing the corresponding esds in ligand CIF file. By making the esds smaller you will make the corresponding restraints stronger.
But in general it is dangerous to do, and normally is not recommended. If you make the esds too small, that means the corresponding contribution to overall restraints target arising from that ligand will be overwhelmingly large, so the restraints from other atoms will be negligibly small. In practice this means you will get a model with distorted geometry. This is exactly why often the CIF files created by PRODRG do not work well with phenix.refine (since it sometimes puts very small esds, which explodes refinement).
Pavel
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-- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
participants (2)
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Pavel Afonine -
Yarrow Madrona