On observation is that I have a brand new pipeline for this that will be released as soon as the main distribution has gemmi installed…this is based on far newer code developed by John Berrisford and Eugene Krissinel. It does, however, still rely on a zero cycle REFMAC run...
On 3 Oct 2018, at 12:16, Martin Noble <martin.no...@newcastle.ac.uk<mailto:martin.no...@newcastle.ac.uk>> wrote: I will check that there is not a new keyword that needs to be set for TLS to be used as provided. M. On 3 Oct 2018, at 12:09, Christian Roth <christianroth...@gmail.com<mailto:christianroth...@gmail.com>> wrote: 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 <antonio.ar...@path.ox.ac.uk<mailto: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<mailto: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<mailto:christianroth...@gmail.com>> Sent: 02 October 2018 20:52 To: Antonio Ariza; CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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 ________________________________ 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
