Are downstream users of models with poorly resolved regions more likely to spot them if they have huge B-factors or zero occupancy? If the answer is 'neither', then perhaps we need to develop a different solution.
On Fri, 10 Mar 2023 at 16:33, Goldman, Adrian <adrian.gold...@helsinki.fi> wrote: > Maybe simplest just to trim it back. I do worry that the presence of a > wrong conformation will lead to inaccurate vdw clashes that could > negatively affect other atoms. > > Sent from my iPhone > > > On 10 Mar 2023, at 18:25, Phil Jeffrey <pjeff...@princeton.edu> wrote: > > > > On 3/10/23 4:05 AM, Julia Griese wrote: > >> Hi all, > >> My impression has been that the most common approach these days is to > “let the B-factors take care of it”, but I might be wrong. Maybe it’s time > to run another poll? > >> Personally, I call any other approach R-factor cosmetics. The goal in > model building is not to achieve the lowest possible R-factors, it’s to > build the most physically meaningful, most likely to be correct, model. > > > > And I could call your approach "model cosmetics". > > > > If you can't see the side-chain, you don't know where it is and you > probably don't even know where the centroid of the distribution is. Only in > the case of very short side-chains with few rotamers can you make a > reasonable volume approximation to where the side-chain is and "let the > B-factors" smear out the density to cover a range of the projected > conformations. > > > > For longer side-chains, if you put it in a single conformation, you are > very likely NOT coming close to correctly modeling the actual distribution > of the conformations. So let's circle back on "most likely to be correct > model" and ask what we *actually* know about where the atoms are. > > > > Put your disordered Arg in with 10 alternate conformations, each with a > refined relative occupancy, and then let the B-factors smear that lot out, > and that's your better model. > > > > Phil Jeffrey > > Princeton > > > > ######################################################################## > > > > 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 > > 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/ > -- Dr Jon Agirre [image: A button with "Hear my name" text for name playback in email signature] <https://www.name-coach.com/jon-agirre> Royal Society University Research Fellow CCP4 WG2 co-chair and ED&I champion | instruct-ERIC representative @ 3D-Bioinfo (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8252 Mastodon: @glycojones@mastodon.world ######################################################################## 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/
