Re: [phenixbb] refinement with alternative molecules?
Hi Ralf, I've done the refinement with alt. conf.. The occupancy is 0.58 for Mol A, 0.42 for Mol B. The maps look OK. R-factors drops a little bit. Before when I put Mol A in that region for refinement, I saw additional densities (a helix) for Mol B. When I put Mol B in the region for refinement, I saw additional densities (loops) for Mol A. Now with alt. conf. there are no additional densities. Can I use the occupancies for publication? Or do I need to do/check something else? Thanks! Su-Chang
Hi Su-Chang,
I will try to refine the structure without NCS restraints. I'd be interested to know how it goes, although I'm too busy to get into the NCS code right now. If the resolution is low I'd think it is better to use NCS, without alt. conf. The mismatches you saw between related molcules may be pure artifacts. But trying is better than guessing! Ralf
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Su-Chang,
I've done the refinement with alt. conf.. The occupancy is 0.58 for Mol A, 0.42 for Mol B. The maps look OK. R-factors drops a little bit.
Before when I put Mol A in that region for refinement, I saw additional densities (a helix) for Mol B. When I put Mol B in the region for refinement, I saw additional densities (loops) for Mol A. Now with alt. conf. there are no additional densities.
Interesting. I'll keep this in mind for future work on the NCS code (it was developed before I had a good grip on alt. confs.)
Can I use the occupancies for publication?
Seems all right to me. I'm guessing referees may ask for R-factors without alt. conf. but using NCS. Ralf
Hi Su-Chang, that's interesting indeed. I would love to have a look at this structure: whether when it's published, or you don't mind sending it to me directly. Pavel. On 1/28/10 1:15 AM, Su-Chang Lin wrote:
Hi Ralf, I've done the refinement with alt. conf.. The occupancy is 0.58 for Mol A, 0.42 for Mol B. The maps look OK. R-factors drops a little bit.
Before when I put Mol A in that region for refinement, I saw additional densities (a helix) for Mol B. When I put Mol B in the region for refinement, I saw additional densities (loops) for Mol A. Now with alt. conf. there are no additional densities.
Can I use the occupancies for publication? Or do I need to do/check something else?
Thanks! Su-Chang
Hi Su-Chang,
I will try to refine the structure without NCS restraints.
I'd be interested to know how it goes, although I'm too busy to get into the NCS code right now. If the resolution is low I'd think it is better to use NCS, without alt. conf. The mismatches you saw between related molcules may be pure artifacts. But trying is better than guessing! Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Su-Chang Lin