Hi Pavel, It is very rarely sensible to disagree with automation, definitely in this case. My problem was that the automated NCS was including bits that were clearly violators of NCS (This was with 1.3 final release). I will be looking forward to any improvements in this respect. Here are a couple questions/suggestions: 1. Does automated NCS picking only work based on the input pdb? Should it not consider electron density maps as well for true automation (which may not be easy to implement)? Otherwise, regions that should eventually be excluded from NCS will be initially restrained, and stay that way cycle after cycle by the automated NCS picking, until some person intervenes and remodels the pdb. Automated analysis of model and electron density for violations of NCS would be a god-send for those large structures with many, many (> 10) NCS chains. (How about a phenix.analyse_complex_ncs instead of phenix.simple_ncs_from_pdb :)) 2. Any automation on restraint weights (possibly based on Rfree behaviour, or something even more complicated)? That would be nice. And definitely not excluding NCS restraints on ADPs (It seems to me commonplace to have one or more NCS related groups to be more "flexible", more "fuzzy". It helps to relax NCS-ADP restraints on those chains). Thanks, Engin On 5/25/09 3:41 PM, Pavel Afonine wrote:
Hi Engin,
since the model gets improved during refinement (hopefully), it is a good idea to update NCS restraints based on improved model, so the default behavior.
The use of NCS restraints in phenix.refine is explained in the manual: http://www.phenix-online.org/documentation/refinement.htm#anch24
I admit that the automatic NCS determination has a room for improvement, but once again: ideally it should be done fully automatically and be updated as model gets improved. It is in my list...
As it is now it's always good to check the automatic choice (as Ralf mentioned).
Pavel.
On 5/18/09 3:33 PM, Engin Ozkan wrote:
Also, don't forget to add ncs.find_automatically=false
I have run many runs with NCS defined with proper syntax, just to be overwritten by NCS derived automatically by phenix, until I realized what was happening. I have always thought that if I define the NCS restraints, phenix should follow it, not try to "improve" upon it. What is the reason for this default behavior?
Engin
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