Hi Phil, I don't think that this is model cosmetics, but I certainly didn't claim that this isn't controversial. That's why we're having this discussion again and again after all.
Have you tried to model a disordered Arg with 10 (why only 10?) alternate rotamers? Did it refine to something sensible? If so, then I would agree that this would be better. I haven't tried it, but I suspect they would all converge more or less on top of each other. (If anyone wants to give it a try, please let me know what happened!) I still maintain that modeling a disordered Arg as an Arg with a single rotamer with high B-factors is more correct than modeling it as an Ala or setting its side chain occupancy to zero, because it is not an Ala, and its side chain atoms are not absent. (Yes, I see Harry's point, but let's assume you've collected your data carefully and don't have such serious radiation damage that you've lost arginine side chains. If that was the case, you'd be missing a whole lot of other side chains too.) I do not claim that such a model accurately reflects where the Arg really is, I only claim that it's the best we can do (at present). Hence why we need to educate users. And absolutely, none of the current solutions is ideal, that's also why we're having this discussion again and again. It seems no one has found a better solution yet. /Julia On 3/10/23, 17:15, "Phil Jeffrey" <pjeff...@princeton.edu <mailto: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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
