Dear All, What follows below is not very specific to the particular program (STAIRSANISO) nor the original questions, but nonetheless, I believe it is relevant.
In the past, performing any adjustments to the diffraction data intended for solving and refining atomic models was more or less considered taboo. When cryo-EM emerged as a competitor to x-ray crystallography, the paradigm began to shift. In cryo-EM, manipulations applied to the data (the map) are a standard practice. The map can be boxed, filtered (sharpened, blurred, etc.), modified (e.g., setting something outside the molecular region), and so forth; you name it. One might wonder why the same isn't done to x-ray data. Historical analogies include truncating data beyond 6-8Å resolution to avoid dealing with the bulk solvent or default sharpening (a feature available in X-plor for some time, then removed for obvious reasons, AFAIK), choosing resolution limits (PAIRREF), and anisotropic data massaging by the UCLA server as a more recent example. STAIRSANISO is the leader in doing things along these lines as of today. Indeed, why not if this is helpful to solve the structure? However, it's important that the deposition clearly contains and annotates at least the following: - the original unmanipulated data; - modified data (by whatever method or program); - accessible information about the data that was used to obtain the final deposited atomic model. Note *accessible* above as this is the key for what follows below. Let's consider this example: https://files.rcsb.org/download/6R72-sf.cif , which is representative of the class of problems I'm trying to convey here. The file has everything, kudos to the authors: The original data, the manipulated data and a whole lot more. Are these data accessible? YES, if you download the file, open it in your favorite text editor, and carefully scroll and read through its 76,566 lines and use your best guess to infer what are the original data arrays, what are the modified data arrays and so on. NO, absolutely NO, if you parse data files in PDB automatically with a script, and attempt to extract particular data (eg., original unmanipulated data). And this is what I find problematic, especially given 215+k entries in PDB as of today. Hope someone does something about it! All the best! Pavel On Tue, Feb 13, 2024 at 4:57 PM Arpita Goswami <bt.arp...@gmail.com> wrote: > Dear all, > > Good day. Thank you all for the very extensive discussions. Both on- and > off-list discussions were very helpful. > > Thank you and a very happy Valentine's day to all.. > > Best regards, > Arpita > > > On Wed, Feb 14, 2024, 01:25 Kay Diederichs <kay.diederi...@uni-konstanz.de> > wrote: > >> Dear readers of CCP4BB, >> >> for various reasons I don't feel inclined to reply to this. >> >> I'm really sorry, >> Kay >> >> On Tue, 13 Feb 2024 15:25:03 +0000, Gerard Bricogne < >> g...@globalphasing.com> wrote: >> >> >Dear Kay, >> > >> ... >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
