Re: [ccp4bb] challenges in structural biology
I will agree with Artem here- Having knowledge as to whether crystallisation is likely or not with a given protein/ complex would be extremely useful. If there were a set of screens/ tests/ experiments that one could run to show that it was 99% certain that something was not going to work (or conversely that something had a good chance of success) would be a goal and substantial step forward for the field. Janet’s point is quite valid here- as we don’t know what people are doing (and we don’t have a defined vocabulary for describing experiments), we don’t actually know what has happened in the past, so it is hard to learn what should be done in the future. So pulling together a defined way of describing what we do is likely the first step to understanding what has been done (and preserving it) so we know what to try in the future. Cheers, tom From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Artem Evdokimov Sent: Monday, 22 July 2019 7:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] challenges in structural biology Dear Kay I disagree that 'magic bullet' is impossible. I think the definition is wrong here - magic bullet to me is a rational set of methods that (when executed with precision and care) enable crystallization to the maximum possible benefit. This includes everything - constructs, crystallization design, etc. Part of the magic bullet is also a precise knowledge when crystallization is unlikely (i.e. an actual proven predictor that consistently discriminates between "you're going to succeed if you work hard" and "it's doomed to fail, don't bother" scenarios in crystallization. The above is not sexy. It does not present itself as a lovely subject on which to have international cocktail parties with politicians delivering fancy speeches. But that is what is needed, and no one is funding that to the best of my knowledge. What needs to be done is a significant amount of testing, standardization, and methods development from the perspective of holistic outcome (i.e. crystals that work) - and none of the previously advertised 'magic bullets' work the way I just described. Having written this, I think you're right - this is a bit of a distraction from James' original point. However it's a valid opportunity for a lively discussion on its own :) Artem - Cosmic Cats approve of this message On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs mailto:kay.diederi...@uni-konstanz.de>> wrote: Dear Artem, black or white is not my way of thinking, which is why I don't believe in Hannibal's approach when it comes to crystallization. None of the magic bullets that were advertised over the past decades have proven generally applicable. I believe more in incremental improvement which in this case includes a few biophysical characterization methods, possibly improved microfluidics or other apparatus, and expanded screens. And a lot of hard work, perseverance, intuition, frustration tolerance. Nothing that really needs huge funding - of course it does need money, but just a share of what is anyway needed for the usual lab work including expression, purification, functional characterization, binding studies and the like. One area where a huge amount of money was burnt is crystallization in space, on board of e.g. the spacelab and ISS. This is for me an example of a mis-led approach to throw money at a difficult problem, with the expectation of a solution. Science does not work like that, and money in this case seems more to be the problem than the solution. This example may illustrate a certain failure of us scientists to resist the temptation to promise unrealistic outcomes when confronted with money provided for political reasons, which ultimately undermines our credibility. But this takes us away from James' points. best, Kay On Sun, 21 Jul 2019 16:06:48 -0400, Artem Evdokimov mailto:artem.evdoki...@gmail.com>> wrote: >Dear Kay, > >Even the small, badly diffracting and 'messed up' crystals are still >crystals. There is literally a phase transition (pun very much intended) >between growing *usable crystals* versus *having no crystals* (or having >crystals that do not qualify as 'diffraction quality' even under the most >favorable light). Points 2-9 fall into the 'I have crystals' bucket and >everything else is in the 'I have no crystals' bucket. > >I am being deliberately black and white of course. > >As to whether huge funding would help to bridge the 'phase gap' - to me >this is a purely theoretical question since to the best of my knowledge >there never was a 'huge funding' for this particular problem :) And if it >is true that the general belief in the art is that crystallization is not >worth investing into because there's no hope in it then of course it is a >self-fulfilling prophesy. > >There is an unresolved dichotomy buried in the sentiment above: it seems >that we (the community of structural biologists) more or less
Re: [ccp4bb] challenges in structural biology
Dear Kay I disagree that 'magic bullet' is impossible. I think the definition is wrong here - magic bullet to me is a rational set of methods that (when executed with precision and care) enable crystallization to the maximum possible benefit. This includes everything - constructs, crystallization design, etc. Part of the magic bullet is also a precise knowledge when crystallization is unlikely (i.e. an actual proven predictor that consistently discriminates between "you're going to succeed if you work hard" and "it's doomed to fail, don't bother" scenarios in crystallization. The above is not sexy. It does not present itself as a lovely subject on which to have international cocktail parties with politicians delivering fancy speeches. But that is what is needed, and no one is funding that to the best of my knowledge. What needs to be done is a significant amount of testing, standardization, and methods development from the perspective of holistic outcome (i.e. crystals that work) - and none of the previously advertised 'magic bullets' work the way I just described. Having written this, I think you're right - this is a bit of a distraction from James' original point. However it's a valid opportunity for a lively discussion on its own :) Artem - Cosmic Cats approve of this message On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear Artem, > > black or white is not my way of thinking, which is why I don't believe in > Hannibal's approach when it comes to crystallization. > > None of the magic bullets that were advertised over the past decades have > proven generally applicable. I believe more in incremental improvement > which in this case includes a few biophysical characterization methods, > possibly improved microfluidics or other apparatus, and expanded screens. > And a lot of hard work, perseverance, intuition, frustration > tolerance. Nothing that really needs huge funding - of course it does > need money, but just a share of what is anyway needed for the usual lab > work including expression, purification, functional characterization, > binding studies and the like. > > One area where a huge amount of money was burnt is crystallization in > space, on board of e.g. the spacelab and ISS. This is for me an example of > a mis-led approach to throw money at a difficult problem, with the > expectation of a solution. Science does not work like that, and money in > this case seems more to be the problem than the solution. > > This example may illustrate a certain failure of us scientists to resist > the temptation to promise unrealistic outcomes when confronted with money > provided for political reasons, which ultimately undermines our > credibility. But this takes us away from James' points. > > best, > > Kay > > On Sun, 21 Jul 2019 16:06:48 -0400, Artem Evdokimov < > artem.evdoki...@gmail.com> wrote: > > >Dear Kay, > > > >Even the small, badly diffracting and 'messed up' crystals are still > >crystals. There is literally a phase transition (pun very much intended) > >between growing *usable crystals* versus *having no crystals* (or having > >crystals that do not qualify as 'diffraction quality' even under the most > >favorable light). Points 2-9 fall into the 'I have crystals' bucket and > >everything else is in the 'I have no crystals' bucket. > > > >I am being deliberately black and white of course. > > > >As to whether huge funding would help to bridge the 'phase gap' - to me > >this is a purely theoretical question since to the best of my knowledge > >there never was a 'huge funding' for this particular problem :) And if it > >is true that the general belief in the art is that crystallization is not > >worth investing into because there's no hope in it then of course it is a > >self-fulfilling prophesy. > > > >There is an unresolved dichotomy buried in the sentiment above: it seems > >that we (the community of structural biologists) more or less believe that > >crystallization research is not fundamentally fruitful (hence the > >no-funding situation). However, anyone who undertakes significant efforts > >to determine an actual structure using crystallography inevitably *has to* > >crystallize their target of interest - and therefore by definition has > hope > >that their particular target will work out, against the overall gloomy > >outlook on the crystallization science as a whole. So we either are a > >collective of self-induced schizophrenics, or the general sentiment is > >wrong and systematic crystallization research is meaningful and > >fruitful - *just > >very very hard*. > > > >In ~200 BC Hannibal reportedly said "I will find a way or make one". I > >think that if we approach problem #1 with this attitude (and an equivalent > >of a very large army's worth in funding) then it can be solved. > > > >Artem > > > >- Cosmic Cats approve of this message > > > > > >On Sun, Jul 21, 2019 at 1:55 PM Kay Diederichs < > >kay.diederi...@uni-konstanz.de>
Re: [ccp4bb] challenges in structural biology
Dear Kay, Even the small, badly diffracting and 'messed up' crystals are still crystals. There is literally a phase transition (pun very much intended) between growing *usable crystals* versus *having no crystals* (or having crystals that do not qualify as 'diffraction quality' even under the most favorable light). Points 2-9 fall into the 'I have crystals' bucket and everything else is in the 'I have no crystals' bucket. I am being deliberately black and white of course. As to whether huge funding would help to bridge the 'phase gap' - to me this is a purely theoretical question since to the best of my knowledge there never was a 'huge funding' for this particular problem :) And if it is true that the general belief in the art is that crystallization is not worth investing into because there's no hope in it then of course it is a self-fulfilling prophesy. There is an unresolved dichotomy buried in the sentiment above: it seems that we (the community of structural biologists) more or less believe that crystallization research is not fundamentally fruitful (hence the no-funding situation). However, anyone who undertakes significant efforts to determine an actual structure using crystallography inevitably *has to* crystallize their target of interest - and therefore by definition has hope that their particular target will work out, against the overall gloomy outlook on the crystallization science as a whole. So we either are a collective of self-induced schizophrenics, or the general sentiment is wrong and systematic crystallization research is meaningful and fruitful - *just very very hard*. In ~200 BC Hannibal reportedly said "I will find a way or make one". I think that if we approach problem #1 with this attitude (and an equivalent of a very large army's worth in funding) then it can be solved. Artem - Cosmic Cats approve of this message On Sun, Jul 21, 2019 at 1:55 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Hi Artem, > > you are certainly correct in that James' points 2-9 would be moot if his > point 1 were solved. But as long as this is not the case, we resort to work > with few and/or small and/or badly diffracting and/or non-isomorphous > crystals, which makes points 2-9 very relevant. > > Maybe the reason why crystallization research is not well funded is that > it is not expected to yield significant improvements. Personally, I think > that even huge funding would not result in methods that succeed in > crystallizing all molecules. > > best, > Kay > > On Sun, 21 Jul 2019 11:28:14 -0400, Artem Evdokimov < > artem.evdoki...@gmail.com> wrote: > > >Excellent question :) > > > >First of all, thank you for putting this out to the community! > > > >Secondly, I agree with several of us who've written that a single > >conference is not enough to discuss all the possible topics. > > > >Thirdly, in my opinion all the other problems are secondary to the main > >(and only remaining!) problem in crystallography: getting > >diffraction-quality protein crystals reproducibly and quickly > > > >The amount of funding for serious crystallization research seems to be > >close to non-existent. In general methodology funding is hard to get, but > >crystallization seems to me like the absolute underdog of the method pool > - > >the true 'red headed stepchild' of the methods development funders. > > > >At risk of repeating myself - the other problems (worthy, significant, and > >urgent as they are!) are subservient to the main issue at hand - namely > >that crystallization remains an unpredictable and artful phenomenon while > >literally all other aspects of structure determination process (the gene > to > >structure pipeline, whatever you might call it)have made astronomic leaps > >forward. > > > >Artem > >- Cosmic Cats approve of this message > > > > > >On Mon, Jul 15, 2019 at 3:44 PM Holton, James M < > >270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote: > > > >> 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
Re: [ccp4bb] challenges in structural biology
Hi All, Agreed! Crystallization methods have improved in some ways, but at least in my experience the real energy barrier is usually knowing enough about the quirky biochemistry of the particular idiosyncratic complex we happen to be working on. That means that one may need a grant's worth of biochemical plans anyway, whether or not "determine structure" is included as an aim (which of course won't get funded unless diffracting crystals are in hand, which is probably an issue for another day ...). Some of the "magic bullets" of the past have turned out to rely on assumptions that remind one of spherical cow jokes. Or to require a very large up-front investment in finicky microfluidics or other technologies that just isn't practical for small labs that try to do biochemistry as well as structure. A long-term worry of mine is training of the next generation: it is quite possible to solve structures now just by pushing buttons in software such as phenix now, and in many cases those suites do make the best decisions, but they deprive learners of understanding what is going on inside the black box. Often I just can't find the relevant tables of statistics, etc to explain to a student why an autosol run produced an ugly map - e.g. cross R factor vs. resolution for native vs. alleged derivative? FOM vs. resolution? Clearly labeled statistics before and after whatever density modification happened? Even a clear, concise log of what kind(s) of density modification were applied? I get frustrated when other people's students can't tell me exactly what they've already tried, but it isn't always their fault. Best, Phoebe ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ On 7/21/19, 12:55 PM, "CCP4 bulletin board on behalf of Kay Diederichs" wrote: Hi Artem, you are certainly correct in that James' points 2-9 would be moot if his point 1 were solved. But as long as this is not the case, we resort to work with few and/or small and/or badly diffracting and/or non-isomorphous crystals, which makes points 2-9 very relevant. Maybe the reason why crystallization research is not well funded is that it is not expected to yield significant improvements. Personally, I think that even huge funding would not result in methods that succeed in crystallizing all molecules. best, Kay On Sun, 21 Jul 2019 11:28:14 -0400, Artem Evdokimov wrote: >Excellent question :) > >First of all, thank you for putting this out to the community! > >Secondly, I agree with several of us who've written that a single >conference is not enough to discuss all the possible topics. > >Thirdly, in my opinion all the other problems are secondary to the main >(and only remaining!) problem in crystallography: getting >diffraction-quality protein crystals reproducibly and quickly > >The amount of funding for serious crystallization research seems to be >close to non-existent. In general methodology funding is hard to get, but >crystallization seems to me like the absolute underdog of the method pool - >the true 'red headed stepchild' of the methods development funders. > >At risk of repeating myself - the other problems (worthy, significant, and >urgent as they are!) are subservient to the main issue at hand - namely >that crystallization remains an unpredictable and artful phenomenon while >literally all other aspects of structure determination process (the gene to >structure pipeline, whatever you might call it)have made astronomic leaps >forward. > >Artem >- Cosmic Cats approve of this message > > >On Mon, Jul 15, 2019 at 3:44 PM Holton, James M < >270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote: > >> 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 >>
Re: [ccp4bb] challenges in structural biology
Hi Artem, you are certainly correct in that James' points 2-9 would be moot if his point 1 were solved. But as long as this is not the case, we resort to work with few and/or small and/or badly diffracting and/or non-isomorphous crystals, which makes points 2-9 very relevant. Maybe the reason why crystallization research is not well funded is that it is not expected to yield significant improvements. Personally, I think that even huge funding would not result in methods that succeed in crystallizing all molecules. best, Kay On Sun, 21 Jul 2019 11:28:14 -0400, Artem Evdokimov wrote: >Excellent question :) > >First of all, thank you for putting this out to the community! > >Secondly, I agree with several of us who've written that a single >conference is not enough to discuss all the possible topics. > >Thirdly, in my opinion all the other problems are secondary to the main >(and only remaining!) problem in crystallography: getting >diffraction-quality protein crystals reproducibly and quickly > >The amount of funding for serious crystallization research seems to be >close to non-existent. In general methodology funding is hard to get, but >crystallization seems to me like the absolute underdog of the method pool - >the true 'red headed stepchild' of the methods development funders. > >At risk of repeating myself - the other problems (worthy, significant, and >urgent as they are!) are subservient to the main issue at hand - namely >that crystallization remains an unpredictable and artful phenomenon while >literally all other aspects of structure determination process (the gene to >structure pipeline, whatever you might call it)have made astronomic leaps >forward. > >Artem >- Cosmic Cats approve of this message > > >On Mon, Jul 15, 2019 at 3:44 PM Holton, James M < >270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote: > >> 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=1 >> > > > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
