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" <[email protected] on behalf of [email protected]> 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 <[email protected]> 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 < >[email protected]> 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&A=1 >> > >######################################################################## > >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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
