I'll shut up soon Other than when asked to review, I consider it best to concern myself most with how I use the share of the limited resources I have access to and refrain from commenting on work by others in fields I have sufficiently little knowledge of that my estimate of worth is likely to be flawed.
I certainly do not agree that a structure determined by EM is a priori more biologically true than one determined by crystallography - as always the only question is exactly what is the structure of, and how has the sample had to be compromised to determine it. If you feel you can prove that this is a flawed statement across the whole of biology - publish an article and we can shut the synchrotrons. Yours - from a mixed-method structural biologist ;-) Susan Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege ________________________________________ From: [email protected] <[email protected]> Sent: 17 July 2019 10:21:42 To: Susan Lea Cc: [email protected] Subject: Re: [ccp4bb] challenges in structural biology Hi Susan, We are not naive if we care about using the limited resources of this planet responsibly. This has nothing to do with whoever's favourite method. I have nothing against crystallography, it is a beautiful art and has been a success historically. I have solved plenty of crystal structures myself and will probably have to keep doing it for a little while. But it is naive to ignore that the time to move on has arrived, and that we have to use resources to develop better technologies which address the real biological questions instead of keeping dinosaurs on life support. How many of the structures solved on synchrotrons worldwide and of the zillions in the PDB are of any use or biological relevance (original question)? There is an enormous amount of waste, including the nasty chemicals use to grow crystals and to phase pointless structures, let's be honest. Best wishes, Radu > I think we are naive if we care about the method used to obtain the structure > - what matters is getting at the structure. What is great is that the variety > of ways we can do this has increased meaning more samples become tractable for > high resolution structure determination. I don’t see the point of ridiculous > my method is better than your method arguments - for some samples all methods > are equivalent, for some there is only one method that will yield answers - we > just need to train students and develop methods that allow the broadest > access. Everything else is bias-driven posturing. Let’s just solve some > structures and learn something about biology. > > > Susan > > Sent from my iPhone > >> On 17 Jul 2019, at 08:43, [email protected] <[email protected]> >> wrote: >> >> Hi Both, >> >> I am not questioning the PDB stats, the issue was whether (crystal) >> structures >> are sufficiently relevant to address biological questions and justify the >> resources. Fragment screening is one example where investment in protein >> crystallography can still be justified (for now). But it doesn't really ask >> or >> answer biological questions... for these, whether we like it or not, >> macromolecular crystallography (or NMR, even in cell) cannot be the future. >> In >> my opinion :-) >> >> Best wishes, >> >> Radu >> >> >>> Stating the crystallography is dead might be a bit premature, it is still >>> king >>> for depositions. >>> >>> >>> >>> In 2017 we had a large number of fragment screening experiments deposited. >>> >>> >>> >>> >>> >>> >>> >>> From: CCP4 bulletin board <[email protected]> On Behalf Of Nukri >>> Sanishvili >>> Sent: 15 July 2019 23:09 >>> To: [email protected] >>> Subject: Re: [ccp4bb] challenges in structural biology >>> >>> >>> >>> I know it is going to hijack the original topic but I could not help... >>> >>> >>> >>> “The reports of death of (macromolecular) crystallography are greatly >>> exaggerated. >>> >>> If we believed the prognosticators, it has been dead since the 80s when >>> some >>> folks made the claim that the only relevant structures were those solved >>> by >>> NMR. >>> >>> I think we've done quite well since then... >>> >>> Best, >>> >>> Nukri >>> >>> >>> >>> On Mon, Jul 15, 2019 at 3:45 PM <[email protected] >>> <mailto:[email protected]> > wrote: >>> >>> Hi Tassos, Tim, >>> >>> I wonder why would you or anyone on this list worry whether biological >>> questions that can be asked and answered with structures are relevant to >>> justify the resources? I think there is abundant evidence that this is the >>> case. Unless your point is that crystallography is now dead for all >>> practical >>> purposes... then yes, I fully agree :-) It would however be wrong to erase >>> its >>> historical contribution to understanding biology. >>> >>> Best wishes, >>> >>> Radu >>> >>> >>>> I would wonder more if the biological questions you can *ask* with a >>>> (crystal) >>>> structure are sufficiently relevant to justify the resources. >>>> >>>> Sent from my iPhone >>>> >>>>> On 15 Jul 2019, at 22:08, Tim Grüne <[email protected] >>>>> <mailto:[email protected]> > wrote: >>>>> >>>>> Dear James, >>>>> >>>>> 10) are the biological questions that you can answer with a (crystal) >>>>> structure sufficiently relevant to justify the resources? >>>>> >>>>> Best, >>>>> Tim >>>>> >>>>> >>>>> >>>>> Am 15.07.2019 21:44, schrieb Holton, James M: >>>>>> Hello folks, >>>>>> I have the distinct honor of chairing the next Gordon Research >>>>>> Conference on Diffraction Methods in Structural Biology (July 26-31 >>>>>> 2020). This meeting will focus on the biggest challenges currently >>>>>> faced by structural biologists, and I mean actual real-world >>>>>> challenges. As much as possible, these challenges will take the form >>>>>> of >>>>>> friendly competitions with defined parameters, data, a scoring system, >>>>>> and "winners", to be established along with other unpublished results >>>>>> only at the meeting, as is tradition at GRCs. >>>>>> But what are the principle challenges in biological structure >>>>>> determination today? I of course have my own ideas, but I feel like >>>>>> I'm >>>>>> forgetting something. Obvious choices are: >>>>>> 1) getting crystals to diffract better >>>>>> 2) building models into low-resolution maps (after failing at #1) >>>>>> 3) telling if a ligand is really there or not >>>>>> 4) the phase problem (dealing with weak signal, twinning and >>>>>> pseudotranslation) >>>>>> 5) what does "resolution" really mean? >>>>>> 6) why are macromolecular R factors so much higher than small-molecule >>>>>> ones? >>>>>> 7) what is the best way to process serial crystallography data? >>>>>> 8) how should one deal with non-isomorphism in multi-crystal methods? >>>>>> 9) what is the "structure" of something that won't sit still? >>>>>> What am I missing? Is industry facing different problems than >>>>>> academics? Are there specific challenges facing electron-based >>>>>> techniques? If so, could the combined strength of all the world's >>>>>> methods developers solve them? I'm interested in hearing the voice of >>>>>> this community. On or off-list is fine. >>>>>> -James Holton >>>>>> MAD Scientist >>>>>> ######################################################################## >>>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB >>>>>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 >>>>> >>>>> -- >>>>> -- >>>>> Tim Gruene >>>>> Head of the Centre for X-ray Structure Analysis >>>>> Faculty of Chemistry >>>>> University of Vienna >>>>> >>>>> Phone: +43-1-4277-70202 >>>>> >>>>> GPG Key ID = A46BEE1A >>>>> >>>>> ######################################################################## >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB >>>>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB >>>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 >>>> >>> >>> >>> -- >>> Radu Aricescu >>> MRC Laboratory of Molecular Biology >>> Francis Crick Avenue >>> Cambridge Biomedical Campus >>> Cambridge CB2 0QH, U.K. >>> tel: +44-(0)1223-267049 >>> fax: +44-(0)1223-268305 >>> www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB >>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 >>> >>> >>> >>> _____ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB >>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 >>> >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> >> >> -- >> Radu Aricescu >> MRC Laboratory of Molecular Biology >> Francis Crick Avenue >> Cambridge Biomedical Campus >> Cambridge CB2 0QH, U.K. >> tel: +44-(0)1223-267049 >> fax: +44-(0)1223-268305 >> www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu >> >> ######################################################################## >> >> 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 > -- Radu Aricescu MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44-(0)1223-267049 fax: +44-(0)1223-268305 www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
