Hello, yes, the trimming and occupancy tricks can be confusing and they can be a bit of a cheeky way to improve the model statistics. I prefer to build the whole side chain and if you can't see all or part of it, then that's just too bad, but I have erred.
Best wishes, Jon Cooper. [email protected] Sent from Proton Mail mobile -------- Original Message -------- On 10 Mar 2023, 01:25, Rhys Grinter wrote: > 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 ######################################################################## 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/
