Refinement with optimize weights
Hello Forum, I am using Phenix 1.7.1-743 to refine my structure. My R/Rfree values for a 2.5 A structure were 0.22/0.305. I used optimize weights along with TLS and the R/Rfree values improved to 0.23/0.29. I wanted to know what parameters should I use for subsequent refinement. I read on phenix bb that one needs to fix the wxc_scale and wxu_scale. Is this correct? What values should be used for these parameters after running optimize wxc/wxu weights. Is there any place where I can get starting values for my future refinement? Also, I would like to know what Fix X-ray/stereochemistry weight and Fix X-ray/ADP weights are for? Thanks for the help.
Hello, have a look at "Improved target weight optimization in phenix.refine" article here: http://www.phenix-online.org/newsletter/ and, make sure you are using the latest version of PHENIX - this is essential: http://www.phenix-online.org/download/nightly_builds.cgi
I wanted to know what parameters should I use for subsequent refinement.
Which parameters do you mean? Optimal weights are determined per refinement run. It is not given that in a next refinement run the optimal weights will be the same as in previous one. Since weights optimization takes a long time to run (if you have multiple cpu machine then it can be run in parallel), normally you run it towards the end of refinement and not all the way through.
I would like to know what Fix X-ray/stereochemistry weight and Fix X-ray/ADP weights are for?
In case you have your own weight values, you can specify them and then phenix.refine will use them as is. Pavel
participants (2)
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Ankit Gupta -
Pavel Afonine