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 <antonio.ar...@path.ox.ac.uk> 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: *antonio.ar...@path.ox.ac.uk > *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> > > > ------------------------------ > *From:* Christian Roth <christianroth...@gmail.com> > *Sent:* 02 October 2018 20:52 > *To:* Antonio Ariza; CCP4BB@JISCMAIL.AC.UK > *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: *antonio.ar...@path.ox.ac.uk > *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> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
