Hi This is why I put “rigid” and “flexible” in quotes in my original post - to allow people to put whatever interpretation on them that they chose (within limits)!
Of course, it’s always best to try to use the correct terms in a scientific discussion, but we all use shorthand; e.g., in crystallography we’re (mostly) happy to talk about “reflections” (even Lawrence Bragg did, but spelt it with an “x” not “ct”) when we all know that they aren’t specular reflections, which is what most people (including physicists) mean by the word… Harry > On 26 May 2021, at 22:06, Dale Tronrud <de...@daletronrud.com> wrote: > > Dear Boaz, > > We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) > arise from their flexibility, ..." This makes it sound like you agree that > these deficiencies in other regions may be caused by properties other than > flexibility. > > As an extreme example, the N-terminal region of a protein may have a broad > distribution in the ensemble model either because this region experiences > many conformations in solution, or because this peptide was cleaved from the > protein at some earlier time and its absence was not recognized by the > experimentalist. > > Dale Tronrud > > On 5/26/2021 1:06 PM, Boaz Shaanan wrote: >> Hi Dale and Cecil, >> This is quite a circular argument, isn't it? Deficient NOE's for some >> regions (e.g. loops) arise from their flexibility, hence they are not as >> well resolved as other (e.g. internal ) regions for which the number of NOE >> is large. So they are flexible by all accounts and, not surprisingly, align >> usually with high B-factor regions in the corresponding crystal structures. >> In cases where such flexible regions are held by crystal contacts the >> situations would likely be different. >> Cheers, >> Boaz >> /Boaz Shaanan, Ph.D. >> Dept. of Life Sciences >> Ben-Gurion University of the Negev >> Beer-Sheva 84105 >> Israel >> E-mail: bshaa...@bgu.ac.il >> Phone: 972-8-647-2220 >> Fax: 972-8-647-2992 or 972-8-646-1710 / >> // >> // >> / >> / >> ------------------------------------------------------------------------ >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale >> Tronrud <de...@daletronrud.com> >> *Sent:* Wednesday, May 26, 2021 10:46 PM >> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles >> I agree with Dr Breyton. The variability in an NMR ensemble does not >> reflect "mobility" but simply "uncertainty" in conformation. The spread >> in coordinates in some regions simply reflects the lack of experimental >> data which could define a single conformation. There are many reasons >> why these data are be absent and high mobility is only one. >> Dale Tronrud >> On 5/26/2021 8:45 AM, Cécile Breyton wrote: >>> Hello, >>> In my understanding of NMR, the loops and terminii that adopt very >>> different conformations in the structure ensemble rather reflect the fact >>> that for those residues, the number of constraints is lower, thus the >>> number of structures that fulfil the constraints is larger.... A dynamics >>> study of the protein will be much more informative. >>> Cécile >>> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >>>> Hi Harry, >>>> >>>> The superpose/overlay of all the structures in PyMol should inform you the >>>> rigid part of the protein as well as the flexible part. The rigid part >>>> would have very low backbone RMSD or overlay tightly and the flexible part >>>> (loops, N-term and C-term etc.) would not superpose tightly. If you check >>>> literature, the dynamics of the protein may have been studied through NMR >>>> relaxation. >>>> >>>> Smita >>>> >>>> >>>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>> >>>> >>>> Hi >>>> >>>> Given that there are plenty of people on this BB who are structural >>>> biologists rather than “just” crystallographers, I thought someone here >>>> might be able to help. >>>> >>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>> structures that fit the NOEs, is there a tool available that will give me >>>> some idea about the bits of the structure that do not vary much (“rigid”) >>>> and the bits that are all over the place (“flexible”)? >>>> >>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>> something that could add a figure to the B columns in a PDB file so I >>>> could see something in QTMG (or PyMol if forced…) or do other useful >>>> things with the information. >>>> >>>> Harry >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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 >>>> <http://www.jiscmail.ac.uk/CCP4BB>, a >>>> mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, >>>> terms & conditions are >>>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://www.jiscmail.ac.uk/policyandsecurity/> >>>> <https://www.jiscmail.ac.uk/policyandsecurity/ >> <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 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >>>> >>> ------------------------------------------------------------------------ >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >> ######################################################################## >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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 >> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <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/
