Hi Boaz, I see your point in regards to making a database of "all" diffraction images. The argument I clearly failed to make effectively was that improvement of structures can frequently yield useful biological information which is why I believe that, at the least, images of deposited structures should be archived. The availability of the structure factors alone can allow crystallographers to improve models significantly, but there is always the question of whether there was more data lost to button smashing despite developers efforts to make data processing idiot-proof.
If I am going to invest years of my life and millions of tax dollars on a hypothesis derived from a structure I personally would be willing to take a day to reprocess the images and put the model through it's paces to ensure that I'm not wasting my time and/or other people's money. Yes experimenters (including myself) make mistakes, but the joy of crystallography is that we can effectively backtrack, identify where the mistake was made, fix it and learn from it. All it costs us is a couple of hours and perhaps a little pride whereas the result is stronger more effective science for our field as a whole. In my mind that equalizes out the cost:benefit ratio considerably. Of course this is all just my opinion, Katherine 2011/10/28 Boaz Shaanan <bshaa...@exchange.bgu.ac.il> > Hi Katherine, > > It sounds as if you had all you needed to correct other people's (and your > own) errors, as you described, in the existing database (EDS, PDB) or your > own data, right? That hardly justifies establishing a new database of which > at least 80-90% is worthless. Furthermore, since much of the non-indexable > data arise from experimenter's faults, is it not the time to start a > discussion (preferably prior to setting up a committee) on deposition of > crystals so that anybody can have a go at them to detect problems if they > wish? > > 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 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 * > ** > ** > * > > * > ------------------------------ > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Katherine > Sippel [katherine.sip...@gmail.com] > *Sent:* Friday, October 28, 2011 8:06 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] raw data deposition > > Generally during these rigorous bb debates I prefer to stay silent and > absorb all the information possible so that I can make an informed decision > later on. I fear that I am compelled to contribute in this instance. In > regards to the "does this make a difference in the biological interpretation > stage" issue, I can state that it does. In my comparatively miniscule career > I have run into this issue three times. The first two address Adrian's > point... > > And (b) even if they do, is this continual improvement even worthwhile? >> I am always depressed at how little a model changes from an initial build >> to the final one, even when the rfree drops from 35 to 23. All that work! - >> and my biological interpretation would have been almost the same at the >> beginning as at the end. >> > > In one instance I adopted an orphaned structure and ran it through a > slightly more advanced refinement protocol (on the same structure factors) > and ended up with a completely different story than the one I started with > [1]. Another researcher in my grad lab identified mis-oriented catalytic > residues in an existing structure from EDS server maps which affects the > biochemistry of the catalytic mechanism [2]. > > In another case I decided that I would reprocess some images that I had > originally indexed and scaled in my "Ooo buttons clicky clicky" stage of > learning crystallography and the improved structure factors revealed a > alternate conformations for both a critical loop and ligand orientation [3]. > > And this was all in the last 4 years. So I would posit that the answer is > yes there are significant biological insights to be had with the capacity to > reassess data in any form. > > Katherine > > [1] J Phys Chem Lett. 2010 Oct 7;1(19):2898-2902 > [2] Acta Crystallogr D Biol Crystallogr. 2009 Mar;65(Pt 3):294-6. > [3] Manuscript in progress > > ------------ > Katherine Sippel, PhD > Postdoctoral Associate > Baylor College of Medicine >
