Re: [ccp4bb] raw data deposition

[Boaz Shaanan]

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