phenix.refine : desire less conservative bonds and angles in optimize_wxc = True.
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 gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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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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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--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis,
I'm still refining against experimental phases.. would that matter?
it's a good thing to do in general, but I have no idea how this would be connected to what we observe. So, I don't know the answer, but I do know how to get it: simply repeat the same refinement run using ML target (without using phases) and see if there is any difference. Make sure you use the same starting model in both runs (so you can do meaningful comparison). I would be interested to know the outcome... All the best! Pavel.
participants (2)
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Francis E Reyes -
Pavel Afonine