Pavel I'm still refining against experimental phases.. would that matter? The reason I ask is because in my 2fofc maps, there's density that can possibly be accommodated by not being so strict in the backbone (this is a nucleic acid). F On Jan 18, 2011, at 1:59 PM, Pavel Afonine wrote:
Hi Francis,
both bond and angle rmsds did not change much for a broad range of target weight scales - from 0.5 to 10: for all trial values they stayed approximately the same 0.001/0.4. Interestingly, the Rfree did change much too, although it keeps slightly dropping till wxc_scale=10. Hm... first of all, this is a bit unusual so I wonder if there is anything special about your data/model? Also, I wonder what if we let the procedure go beyond wxc_scale=10? Unfortunately, it's not a parameter and "10" is hardwired somewhere in the code... But if you send me the data and model I will be able to change the code and try it myself.
Alternatively, you can just try manually a few values, like wxc_scale= 15, 20, 25, .. until it stops making sense -:)
Pavel.
On 1/18/11 12:35 PM, Francis E Reyes wrote:
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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