[phenixbb] help with geometry target weight
Brown, Breann
Breann_Brown at brown.edu
Thu Mar 18 11:49:12 PDT 2010
I am currently refining a structure at 2.4A resolution. I would like to increase the geometry target weight during refinement, however when I decrease wxc_scale (to 0.25 or 0.1) there is no change in the bond deviations or R factors compared to refinement with the default wxc_scale. I noticed in the refinement logfile under XYZ refinement wc=0. This does not change when I change the wc value in the command line (wc=2.0 for example) as suggested in a previous email. I also see no change when I use the optimize_wxc=true command. Examples of the command line input and output log files are below. I am currently using version 1.6-289 and would appreciate any help in resolving this issue as it seems the geometry is not being properly weighted during refinement.
Thanks,
Breann
Breann L. Brown
Department of Molecular Pharmacology, Physiology and Biotechnology
Brown University
Box GE-3
Providence, RI 02912
>phenix.refine data.mtz model.pdb ligand.cif twin_law strategy=tls+individual_adp tls.params main.ncs=true wxc_scale=0.1 wc=2.0
========================== Target weights: x-ray data =========================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc |
| wxc = 1.000000 wxc_scale = 0.100 wc = 0.000 |
| angle between x-ray and geometry gradient vectors: None (deg) |
| |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu |
| wxu = 11.057053 wxu_scale = 2.160 wu = 1.000 |
| angle between Xray and ADP gradient vectors: 143.484 (deg) |
|-----------------------------------------------------------------------------|
------------------------------------------------------------------------
stage angl bond chir dihe plan repu geom_target
0 : 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
1_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
1_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
2_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
2_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
3_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
3_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
4_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
4_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
5_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
5_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
6_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
6_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
7_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
7_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
8_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
8_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
9_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
9_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
10_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01
------------------------------------------------------------------------
Maximal deviations:
stage angl bond chir dihe plan repu |grad|
0 : 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
1_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
1_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
2_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
2_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
3_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
3_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
4_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
4_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
5_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
5_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
6_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
6_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
7_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
7_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
8_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
8_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
9_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
9_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
10_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01
-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
Sent: Tuesday, February 23, 2010 1:40 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] weights optimization, add hydrogens
Hi Ursula,
> I am refining a 2.0 A structure in Phenix using mostly the graphical
> interface. The maps are very good and the R factors are low
> (0.208/0.173). But the geometry is not so great with bond deviations
> of 0.208 and Angle deviations of 1.85. What is the best thing to do
> to try to improve the geometry. Should I try to optimize the weights?
the R-factors seem good indeed. Yes, Although the angle deviations seem
ok to me, I'm concerned about the bond deviations... Yes, you can try
two things:
- increase the restraints strength by increasing the corresponding weight:
from the command line: "wc=VALUE", where VALUE is a number somewhat
larger than 1.0;
from the GUI:
Refinement settings -> All parameters -> Refinement target weights...
-> Stereochemistry weight scale
- Run automatic weight optimization (note, this may take a while to run):
from the command line: use keyword: "optimize_wxc=true";
from the GUI:
Refinement settings -> All parameters -> Refinement target weights...
-> Optimize X-ray/stereochemistry weight
Alternatively, you can send me your PDB and data file and I will tell
you what exactly is not right and how to fix it.
Pavel.
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