That was my thought exactly. Eleanor has been faster. Indeed if the TLS
parameters get not passed to the refmac subjob it will not be taken into
account. It did work previously, but there have been some changes
recently and it might be that there is something broken now. It would be
good to check this, because it should be fixed.
Christian
Am 03.10.2018 um 11:53 schrieb Eleanor Dodson:
That is a serious bug in the deposition task.
You can find the refmac command script if you search in the Job list
directories. If it does not invoke TLS when there are TLS records
provided that is a fixable bug..
Eleanor
On Wed, 3 Oct 2018 at 10:51, Antonio Ariza
<[email protected] <mailto:[email protected]>> wrote:
Hi Christian,
Yes, I used TLS refinement for all the structures I deposited …
but the TLS parameters were included in the deposition task, so I
assumed the programme would know that it needs to take these into
account.
Anyway … I guess that in order to correct the remarks in the
headers of the curated coordinates in the PDB, I'll have to alter
all the cif files manually and then resubmit them to the
deposition server.
Cheers,
Tony
------------------------------------------------------
*
Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE*
*e-mail: *[email protected]
<mailto:[email protected]>
*Tel: 00 +44 1865 285655*
**
*Links to my public profiles:*
ResearchGate <https://www.researchgate.net/profile/Antonio_Ariza>
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GoogleScholar
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Twitter <https://twitter.com/DrAntonioAriza?lang=en>
*Check out my latest paper!!!*
Structural insights into the function of ZRANB3 in replication
stress response <http://www.nature.com/articles/ncomms15847>
------------------------------------------------------------------------
*From:* Christian Roth <[email protected]
<mailto:[email protected]>>
*Sent:* 02 October 2018 20:52
*To:* Antonio Ariza; [email protected]
<mailto:[email protected]>
*Subject:* Re: [ccp4bb] conversion from pdb to cif format changes
R factors ... why?
Hi Tony,
is that for all structures or just some? I recall there was a
problem when one has used TLS refinement. The deposition task runs
a 0 cycle refmac job to recreate the statistics. If there is a
difference, e.g no TLS included that might explain the difference.
Cheers
Christian
Am 02.10.2018 um 19:25 schrieb Antonio Ariza:
Hi all,
I'm wondering if anyone else has noticed this ... or is there
something I am missing here?
One of the reviewers of my latest manuscript just pointed out
that the R factors in my validation reports are significantly
different (i.e. worse) than those I stated in the paper. So, I
checked and indeed they are. I tracked the difference in the
numbers down to the point where I used "Prepare files for
deposition" in ccp4i2. This is the first time I used this
programme to convert my pdb and mtz files into cif files, instead
of trying to deposit the pdb and mtz files as I've always done.
The conversion, however, changed the R factors ... and seemingly
nothing else as the coordinates of both files are still the same.
Any idea why the programme does this? Is there another programme
I can use that doesn't do this? It's annoying because now I have
to redeposit the data for the 10 structures I've submitted for
this paper.
Here are the remarks of the pdb file and the remarks of the
resulting cif file, as you can see they are the same except for
the R factors.
PDB:
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.13
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.26
REMARK 3 NUMBER OF REFLECTIONS : 35463
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.20233
REMARK 3 R VALUE (WORKING SET) : 0.20068
REMARK 3 FREE R VALUE : 0.23658
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.7
REMARK 3 FREE R VALUE TEST SET COUNT : 1759
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH : 1.670
REMARK 3 BIN RESOLUTION RANGE LOW : 1.714
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2221
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.65
REMARK 3 BIN R VALUE (WORKING SET) : 0.392
REMARK 3 BIN FREE R VALUE SET COUNT : 113
REMARK 3 BIN FREE R VALUE : 0.390
CIF:
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.13
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.26
REMARK 3 NUMBER OF REFLECTIONS : 35463
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.24316
REMARK 3 R VALUE (WORKING SET) : 0.24133
REMARK 3 FREE R VALUE : 0.28140
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.7
REMARK 3 FREE R VALUE TEST SET COUNT : 1759
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH : 1.670
REMARK 3 BIN RESOLUTION RANGE LOW : 1.714
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2221
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.65
REMARK 3 BIN R VALUE (WORKING SET) : 0.426
REMARK 3 BIN FREE R VALUE SET COUNT : 113
REMARK 3 BIN FREE R VALUE : 0.429
Cheers,
Tony
------------------------------------------------------
*
Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE*
*e-mail: *[email protected]
<mailto:[email protected]>
*Tel: 00 +44 1865 285655*
**
*Links to my public profiles:*
ResearchGate <https://www.researchgate.net/profile/Antonio_Ariza>
LinkedIn <https://www.linkedin.com/in/antonioariza1>
GoogleScholar
<https://scholar.google.co.uk/citations?user=9pAIKV0AAAAJ&hl=en>
Twitter <https://twitter.com/DrAntonioAriza?lang=en>
*Check out my latest paper!!!*
Structural insights into the function of ZRANB3 in replication
stress response <http://www.nature.com/articles/ncomms15847>
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