Hi, first of all I would suggest to use the latest available PHENIX. This will make sure you get rmsd and not mean values for the deviations from ideal stereo-chemistry. CCI Apps is out of date right now, so the best if you use phenix.refine from the latest PHENIX installer (1.3 beta pre-release version). You can look at the NEW updated phenix.refine documentation here: http://www.phenix-online.org/new-site/documentation/refinement.htm It has more examples and general information than previous version. In particular, it has the answers to all questions that you are asking below. At 2.5A resolution, I wouldn't worry too much about these small values that you get (supposing we look at rmsd): large deviations from ideal values at resolutions close to low (like 2.5A) are hardly justified. Please let me know if you have any more questions! Pavel. Sudharsan Sridharan wrote:
Hi all,
I'm starting to refine a structure using phenix.refine. Almost all my model residues have been built starting from a Sharp map. I've been trying phenix.refine with and without SA and getting bond angle rmsds of 1.0 -1.1 (2.5 A data, using mlhl targets; example below) (yet to add water and also trying water picking in phenix.refine). I'm wondering if this sounds low (I have read discussions on bond and angle rmsds). More importantly I'd like to know how to work with different parameters (weights etc) during refinement in phenix. Could you please point to what params are safe to manipulate.
Thanks, Sid.
REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.3637 r_free = 0.4003 bonds = 0.010 angles = 1.175 REMARK Final: r_work = 0.2607 r_free = 0.3236 bonds = 0.007 angles = 1.017 REMARK ************************************************************************ _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb