Re: [ccp4bb] help with wwPDB validation warning
Ok - I have tracked down where it is coming from. The value being reported is sum(I)/sum(sigma_I). This is not the same as Mean(I/sigmaI) - as I interpret the later as (Sum(I/sigma))/n. Where I comes from is the intensity_meas, intensity_meas_au, or intensity column - whichever is present (priority left to right). No averages here. It is a simple diagnostic >80 or < 2 - report a warning. This is from the old sf_convert program (written > 15 years ago) and the various warnings were carried over to a re-implementation in python. At the time the program was implemented, the PDB had only started trying to make sense of the experimental data provided by the authors. Remember, experimental X-ray data were not required by the PDB until 2008. Prior to that the data were optional, and some are a mess. Use of experimental data in validation came afterwards. MTZ files might have been accepted back then (I cannot remember) - so ensuring that the conversion did not result in incorrect translation was important. The person doing the work at the time was a structural biologist, but may have come up with his own analyses to find conversion issues. There will likely not be a reference. Certainly the sources do not reference a methodology here. So - what can we do moving forward? Using community standards for identification of such errors should be incorporated. Changing the code is relatively easy. Choosing the correct formulas would be the most meaningful. And if sf_convert reports different data from AIMLESS - we should strive to understand why. Ezra On 6/10/24 2:15 PM, Gerard Bricogne wrote: Dear Aline, This is an intriguing message: by what exact piece of software was it produced? The notation I_avg/sigI_avg does not appear in the definition of the closest item in the mmCIF dictionary, which would be _reflns_shell.meanI_over_sigI_obs that can be found at https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns_shell.meanI_over_sigI_obs.html As Kay explained, the quantity for which you are getting a warning is a ratio of averages, which is not at all the same as the usual average of (signal-to-noise) ratios, denoted Mean((I)/sd(I)) in AIMLESS. Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense whatsoever in statistical terms. It must be a relic of a quantity that may have seemed like a good idea to someone at some stage, and has since been dutifully carried along forever after, and "gold-plated" so as to still be present in the latest revision of the mmCIF dictionary. Perhaps you could request a reference to the publication in which this quantity was proposed as a validation criterion and its acceptable limits were derived :-) . This being said, if it is indeed the case that the average value of your intensities is smaller than the average of their standard deviations, there is definitely something wrong somewhere. Perhaps a confusion between columns containing values pertaining to intensities vs. amplitudes? To sober me up from all this speculation, Clemens Vonrhein tells me that it is very likely that it is not the I_avg/sigI_avg quantity that is actually being calculated, and that it is simply a "normal" quantity (e.g. Mean((I)/sd(I)) that is being mis-described in the warning message. With best wishes, Gerard. -- On Fri, Jun 07, 2024 at 03:03:30PM +0100, Aline Dias da Purificação wrote: Dear all, I am currently validating a structure for deposition in the wwPDB and encountered the following warning in the validation system: Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo in SF file). The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I didn't understand the warning. Has anyone experienced this before and could assist me? Thank you. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
Re: [ccp4bb] help with wwPDB validation warning
Dear Aline, This is an intriguing message: by what exact piece of software was it produced? The notation I_avg/sigI_avg does not appear in the definition of the closest item in the mmCIF dictionary, which would be _reflns_shell.meanI_over_sigI_obs that can be found at https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns_shell.meanI_over_sigI_obs.html As Kay explained, the quantity for which you are getting a warning is a ratio of averages, which is not at all the same as the usual average of (signal-to-noise) ratios, denoted Mean((I)/sd(I)) in AIMLESS. Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense whatsoever in statistical terms. It must be a relic of a quantity that may have seemed like a good idea to someone at some stage, and has since been dutifully carried along forever after, and "gold-plated" so as to still be present in the latest revision of the mmCIF dictionary. Perhaps you could request a reference to the publication in which this quantity was proposed as a validation criterion and its acceptable limits were derived :-) . This being said, if it is indeed the case that the average value of your intensities is smaller than the average of their standard deviations, there is definitely something wrong somewhere. Perhaps a confusion between columns containing values pertaining to intensities vs. amplitudes? To sober me up from all this speculation, Clemens Vonrhein tells me that it is very likely that it is not the I_avg/sigI_avg quantity that is actually being calculated, and that it is simply a "normal" quantity (e.g. Mean((I)/sd(I)) that is being mis-described in the warning message. With best wishes, Gerard. -- On Fri, Jun 07, 2024 at 03:03:30PM +0100, Aline Dias da Purificação wrote: > Dear all, > > I am currently validating a structure for deposition in the wwPDB and > encountered the following warning in the validation system: > > Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo > in SF file). > > The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I didn't > understand the warning. > > Has anyone experienced this before and could assist me? > > Thank you. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PhD studentship available at Newcastle and Monash University, Australia - fully funded (UK only)
Dear colleagues I’ve got a fully funded PhD studentship (UK only) in my lab and in collaboration with Prof Dena Lyras at Monash University, and I’m reaching out to ask for your help in spreading the word. It's focused on S-layers variants and is a multidisciplinary project, with 2 years at Newcastle University and 1 year at Monash University, Australia. Full stipend at NU and extra funds to support travel and accommodation in Australia (for UK/EU settled status students only). https://www.findaphd.com/phds/project/phd-studentship-in-structural-microbiology-c-difficile-s-layer-variation-from-structure-to-role-in-disease/?p172314 It includes structural biology (crystallography, cryoEM/ET), biochemistry, microbiology (at NU) and infection models (at Monash) so will suit a wide range of backgrounds. Anyone with good lab competency, enthusiastic and willing to learn is welcome, with no particular restrictions of background and biological/structural topics, including chemistry would be suitable. If you know any good students who might be interested, please encourage them to apply or get in touch with me directly. Deadline is July 1st Thanks a lot for your help! Paula === Professor Paula S. Salgado Chair of Structural Microbiology Due to my own work/life balance, my reply might be delayed and you might get emails outside your normal working hours. In any case, I do not expect a response outside those hours. Stay safe. Newcastle University Biosciences Institute Faculty of Medical Sciences 2nd Floor Cookson Building Newcastle University Newcastle upon Tyne, NE2 4HH, UK Tel: +44 (0)191 208 7432 Email: paula.salg...@ncl.ac.uk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
