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Subject:

RE : [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

From:

LEGRAND Pierre <[log in to unmask]>

Reply-To:

LEGRAND Pierre <[log in to unmask]>

Date:

Fri, 28 Oct 2011 17:38:14 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (191 lines)

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 [[log in to unmask]] de la part de Garib N Murshudov [[log in to unmask]]
Date d'envoi : vendredi 28 octobre 2011 17:49
 : LEGRAND Pierre
Cc : [log in to unmask]
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 [[log in to unmask]] de la part de Ed Pozharski [[log in to unmask]]
Date d'envoi : vendredi 28 octobre 2011 16:00
 : [log in to unmask]<mailto:[log in to unmask]>
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:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

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: [log in to unmask]<mailto:[log in to unmask]>
Web http://www.mrc-lmb.cam.ac.uk<http://www.mrc-lmb.cam.ac.uk/>

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