[phenixbb] phenix.refine : desire less conservative bonds and angles in optimize_wxc = True.
Francis E Reyes
Francis.Reyes at Colorado.EDU
Tue Jan 18 12:35:11 PST 2011
Although I specify that I'll allow a max angle rmsd of 2.0
(angles_rmsd_max), optimize_wxc = True results in a limited range of
angles.. for example my optimize_wxc output
Start r_work= 0.2507 r_free= 0.2709 bonds= 0.002 angles= 0.47
r_work= 0.2558 r_free= 0.2728 bonds= 0.001 angles= 0.41
scale= 1.00
r_work= 0.2550 r_free= 0.2725 bonds= 0.001 angles= 0.41
scale= 1.40
r_work= 0.2543 r_free= 0.2724 bonds= 0.001 angles= 0.41
scale= 1.80
r_work= 0.2538 r_free= 0.2723 bonds= 0.001 angles= 0.41
scale= 2.20
r_work= 0.2533 r_free= 0.2721 bonds= 0.001 angles= 0.42
scale= 2.60
r_work= 0.2529 r_free= 0.2721 bonds= 0.001 angles= 0.42
scale= 3.00
r_work= 0.2525 r_free= 0.2721 bonds= 0.001 angles= 0.42
scale= 3.40
r_work= 0.2520 r_free= 0.2720 bonds= 0.001 angles= 0.42
scale= 3.80
r_work= 0.2516 r_free= 0.2719 bonds= 0.001 angles= 0.43
scale= 4.20
r_work= 0.2513 r_free= 0.2719 bonds= 0.001 angles= 0.43
scale= 4.60
r_work= 0.2510 r_free= 0.2718 bonds= 0.001 angles= 0.43
scale= 5.00
r_work= 0.2501 r_free= 0.2717 bonds= 0.002 angles= 0.44
scale= 6.00
r_work= 0.2494 r_free= 0.2718 bonds= 0.002 angles= 0.45
scale= 7.00
r_work= 0.2488 r_free= 0.2716 bonds= 0.002 angles= 0.46
scale= 8.00
r_work= 0.2481 r_free= 0.2715 bonds= 0.002 angles= 0.46
scale= 9.00
r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles= 0.47 scale=
10.00
r_work= 0.2561 r_free= 0.2729 bonds= 0.001 angles= 0.41
scale= 0.85
r_work= 0.2563 r_free= 0.2729 bonds= 0.001 angles= 0.41
scale= 0.70
r_work= 0.2567 r_free= 0.2730 bonds= 0.001 angles= 0.42
scale= 0.55
Final r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles= 0.47
The resolution is about 1.95A and I think the angles/bonds are a
little too tight.
My wxc_scale is currently set to 0.01. Does optimize_wxc use this as a
starting point/does it matter what this value is set to when
optimize_wxc =True ? Is the scale= result in the output really
wxc_scale?
Thanks!
F
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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