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/
