[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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