Hi everyone, I always thought it is better to truncate so that biologists looking at the structures are not misled? Not sure it the best aproach though...
Olga > On 10 Mar 2023, at 02:45, Bernhard Lechtenberg > <[email protected]> wrote: > > Hi Rhys, > > I am also all for leaving side chains and letting the B-factors deal with the > weak/absent density. > > I don’t think there is a consensus, but I kind of remember that somebody did > a poll a few years ago and if I remember correctly the main approaches were > the one described above, or trimming the side-chains. > > Bernhard > > Bernhard C. Lechtenberg PhD > NHMRC Emerging Leadership Fellow > Laboratory Head > Ubiquitin Signalling Division > E [email protected] <mailto:[email protected]> > T +61 3 9345 2217 > > > From: CCP4 bulletin board <[email protected]> on behalf of Rhys Grinter > <[email protected]> > Date: Friday, 10 March 2023 at 12:26 pm > To: [email protected] <[email protected]> > Subject: [ccp4bb] To Trim or Not to To Trim > > Hi All, > > I'm trying to crowdsource an opinion on how people deal with modelling side > chains with poorly resolved electron or cryoEM density. > > My preference is to model the sidechain and allow the B-factors to go high in > refinement to represent that the side chain is flexible. However, I'm aware > that some people truncate sidechains if density is not present to justify > modelling. I've also seen models where the sidechain is modelled but with > zero occupancy if density isn't present. > > Is there a consensus and justifying arguments for why one approach is better? > > Cheers, > > Rhys > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <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 > <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/
