Hmmm - very puzzling.. One expects the <B> for the atoms to more or less match the Wilson B for the data sets..
There are some mini bugs which can mislead you. Is your average a mean or an RMS value? RMS ones can be hugely inflated if you have a few crazily high Bs and the refinement programs can output these. A misplaced LYS can give B factors >>200 - the software is trying to tell you the atoms are not there - but the average B value calculations don't know that! Then if you have refined using TLS the "B factor" associated with each atom is rather poorly defined. Is it a ad on the the vibration described by the TLS or not? And I am sure there are other aberrations I haven't thought of.. Then there is the issue of the initial scaling. Typically we scale all batches to the first for a crystal believing that will be the most ordered.. If you scaled all data sets together you would expect them all then to have more or less the same overall Wilson B. Interesting challenges but the <B> values you quote are bizarre. I presume all the models are the same? Eleanor On Thu, 8 Sept 2022 at 10:41, Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Graeme > > good to know that I haven’t forgotten everything. > > Rgarding the data collection - I don’t think the OP mentioned how many > crystals were used in the data collection (unless, of course, I’ve been > reading even less carefully than normal…). > > Harry > > > On 8 Sep 2022, at 10:29, Winter, Graeme (DLSLtd,RAL,LSCI) < > 00006a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > Hi Harry, > > > > You’re not wrong - “conventional wisdom” these days is pointing to CC of > about 0.3 but I suspect that the difference is pretty modest in general > > > > However, in the case, the difference could have an impact as the higher > resolution reflections may have something to say about the overall B factors > > > > I also wondered about the order of the data collection in this case, > since there will probably be a certain amount of radiation damage across > this number of data sets at non-cryo temperatures > > > > Best wishes Graeme > > > >> On 8 Sep 2022, at 10:21, Harry Powell < > 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > >> > >> hi folks > >> > >> I’ve been away from data processing for a while, but am I alone in > thinking that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of > useful data? I seem to remember that AutoProc and xia2.multiplex use a > default of >= 0.3. > >> > >> Harry > >> > >>> On 7 Sep 2022, at 19:46, Matt McLeod <mjmcleo...@gmail.com> wrote: > >>> > >>> Hi everyone, > >>> > >>> I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), > 313K (2.2A) and I am curious as to the details in determining B-factors. > >>> > >>> I have treated these datasets more-or-less identically for > comparison's sake. I used DIALS to index, integrate, and scale the data. > I scaled the data to a ~0.6 CC1/2 cutoff. > >>> > >>> After fully refining the datasets, there is an odd trend with respect > to temperature (from what has been previously published) and I assume that > this is because of "behind-the-scenes" computation rather than a > biophysical observation. The B-factors slightly decrease from 252-293K, > and then significantly drop at 313K. The maps look pretty well identical > across the datasets. > >>> > >>> 253K - 53.8 A^2 > >>> 273K - 48.4 A^2 > >>> 293K - 45.5 A^2 > >>> 313K - 18.6 A^2 > >>> > >>> I compared the wilson intensity plots from DIALS scaling for 273K and > 313K and they are very comparable. > >>> > >>> I am looking for suggestions as to where to look at how these > b-factors are selected or how to validate that these B-factor are or are > not accurate. Also, any relevant literature would be welcomed. From what > I have read, there is a general trend that as T increase, the atoms have > more thermal energy which raises the b-factors and this trend is universal > when comparing datasets from different temperatures. > >>> > >>> Thank you and happy to supply more information if that is helpful, > >>> Matt > >>> > >>> > ######################################################################## > >>> > >>> 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/ > > > > > > -- > > This e-mail and any attachments may contain confidential, copyright and > or privileged material, and are for the use of the intended addressee only. > If you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > > Any opinions expressed within this e-mail are those of the individual > and not necessarily of Diamond Light Source Ltd. > > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > > Diamond Light Source Limited (company no. 4375679). Registered in > England and Wales with its registered office at Diamond House, Harwell > Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > ######################################################################## > > > > 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 hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
