Thanks all for your suggestions,
Here's a little summary of my recent tests.
I am currently using "WEIGHT AUTO" and BREF MIXED with a pdb file that contains
ANISOU definition for all atoms except hydrogens.
Final results for "BREF MIXED" refinement :
Initial Final
R factor 0.0880 0.0867
R free 0.0932 0.0925
Rms BondLength 0.0174 0.0189
Rms BondAngle 2.8613 2.8740
Rms ChirVolume 0.1076 0.1146
Final results for "BREF ANISO" refinement:
Initial Final
R factor 0.0880 0.0874
R free 0.0932 0.0956
Rms BondLength 0.0174 0.0189
Rms BondAngle 2.8613 2.8683
Rms ChirVolume 0.1076 0.1151
In the "WEIGHT AUTO" run refmac5 uses: "Weight matrix 137.7641"
Final results for "WEIGHT MATRIX 60" refinement:
Initial Final
R factor 0.0880 0.0872
R free 0.0932 0.0922
Rms BondLength 0.0174 0.0181
Rms BondAngle 2.8613 2.8632
Rms ChirVolume 0.1076 0.1134
I have just sent Garib different data files so that he can reproduce the
problem one can have with H naming/dictionaries definitions.
When it happens, from the same initial pdb with "WEIGHT AUTO" and "BREF MIXED"
but a differente cif definition (from the latest refmac_dictionary_v5.31) here
what it gives:
Initial Final
R factor 0.0880 0.1820
R free 0.0932 0.1869
Rms BondLength 2.8573 2.3884
Rms BondAngle 35.7010 34.7547
Rms ChirVolume 10.5335 4.2429
I hope it helps to clarify the situation,
Cheers,
Pierre
________________________________
De : Garib Murshudov [garib.murshu...@gmail.com] de la part de Garib N
Murshudov [ga...@mrc-lmb.cam.ac.uk]
Date d'envoi : vendredi 28 octobre 2011 17:49
À : LEGRAND Pierre
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
Dear Pierre
Resolution seems to be good enough for full anisotropic refinement. Why don't
you try this and see if it stabilises refinement.
regards
Garib
On 28 Oct 2011, at 16:22, LEGRAND Pierre wrote:
Dear Ed,
Not in my case. I still do *restrained* refinement.
I use:
refi type REST -
resi MLKF -
meth CGMAT -
bref MIXED
ncyc 10
blim 0.1 200.0
With both: weight MATRIX 50 or weight AUTO it gives the same problem.
I have also tested the latest refmac5 version (Refmac_5.6.0119) and latest
dictionaries (refmac_dictionary_v5.31), but it still produce the same error,
directly from the first cycle.
I can give more details and files off-list if requested.
Cheers,
Pierre
________________________________________
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Ed Pozharski
[epozh...@umaryland.edu]
Date d'envoi : vendredi 28 octobre 2011 16:00
À : CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Just to verify, is this by any chance *unrestrained* refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
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Dear Kenneth A. Satyshur,
what is your weight set to? If it is set to 'auto', try setting it to a
specific value and lower that value until the explosion stops.
If this happens at low matrix values (at 1.24A it should be way above 5
or 10 for a well refined structure), your resolution might not be 1.24A,
i.e., you may have integrated noise (check I/sigI over resolution shells).
Tim
P.S.: I wonder what power somebody might have to _force_ you use a
specific software version...
On 10/28/2011 03:48 AM, Kenneth A. Satyshur wrote:
Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24
A,
aniso with H in riding position and it just exploded! I get error in distances
such as
Standard External All
Bonds: 3270 0 3270
Angles: 4923 0 4923
Chirals: 214 0 214
Planes: 368 0 368
Torsions: 957 0 957
---------------------------------------
Number of reflections in file 90428
Number of reflections read 90428
CGMAT cycle number = 1
**** Bond distance outliers
****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 5 PRO C A - A 5 PRO HB1 A mod.= 3.344 id.= 1.329 dev= -2.015
sig.= 0.014
A 5 PRO C B - A 5 PRO HB1 B mod.= 2.997 id.= 1.329 dev= -1.668
sig.= 0.014
A 5 PRO HB1 A - A 5 PRO HG1 A mod.= 2.292 id.= 1.458 dev= -0.834
sig.= 0.021
A 5 PRO HB1 A - A 6 LEU HD23A mod.= 7.407 id.= 0.860 dev= -6.547
sig.= 0.020
A 5 PRO HB1 B - A 5 PRO HG1 B mod.= 2.247 id.= 1.458 dev= -0.789
sig.= 0.021
A 5 PRO HB1 B - A 6 LEU HD23B mod.= 6.529 id.= 0.860 dev= -5.669
sig.= 0.020
A 5 PRO HG1 A - A 5 PRO HD1 A mod.= 2.267 id.= 0.980 dev= -1.287
sig.= 0.020
A 5 PRO HG1 A - A 6 LEU N A mod.= 4.860 id.= 1.530 dev= -3.330
sig.= 0.020
A 5 PRO HG1 A - A 6 LEU HD21A mod.= 6.129 id.= 1.525 dev= -4.604
sig.= 0.021
A 5 PRO HG1 B - A 5 PRO HD1 B mod.= 2.236 id.= 0.980 dev= -1.256
sig.= 0.020
A 5 PRO HG1 B - A 6 LEU N B mod.= 4.922 id.= 1.530 dev= -3.392
sig.= 0.020
A 5 PRO HG1 B - A 6 LEU HD21B mod.= 6.664 id.= 1.525 dev= -5.139
sig.= 0.021
A 6 LEU N A - A 6 LEU CA A mod.= 1.467 id.= 0.970 dev= -0.497
sig.= 0.020
A 6 LEU N A - A 6 LEU HA A mod.= 2.005 id.= 0.970 dev= -1.035
sig.= 0.020
A 6 LEU N A - A 6 LEU CB A mod.= 2.497 id.= 1.530 dev= -0.967
sig.= 0.020
A 6 LEU N B - A 6 LEU CA B mod.= 1.469 id.= 0.970 dev= -0.499
sig.= 0.020
A 6 LEU N B - A 6 LEU HA B mod.= 2.032 id.= 0.970 dev= -1.062
sig.= 0.020
A 6 LEU N B - A 6 LEU CB B mod.= 2.446 id.= 1.530 dev= -0.916
sig.= 0.020
A 6 LEU CB A - A 6 LEU HB2 A mod.= 0.969 id.= 1.521 dev= 0.552
sig.= 0.020
A
Rfree goes form 17 to 28 and R from 15 to 25.
Coot map looks like a bunch of busted insect parts.
I use the exact same input using ccp4 6.1.13 and Refmac 5.5 and all is good. I
am forced to use the
old ccp4 and refmac to publish. Rf 17 R 15.
thanks
--
Kenneth A. Satyshur, M.S.,Ph.D.
Associate Scientist
University of Wisconsin
Madison, Wisconsin 53706
608-215-5207
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk<mailto:jen...@mrc-lmb.cam.ac.uk>
Web http://www.mrc-lmb.cam.ac.uk<http://www.mrc-lmb.cam.ac.uk/>
