I’d say no trimming to side chains for the following reason: There are non-structural biologists using PDB files and if atoms are missing they don’t know what to do. A better approach is where no side chain density allows support of placement, pick the most common rotamer and set the occupancy to zero for those atoms lacking density support. More work for you but more accurate in my opinion.
Jürgen _______________________________________________ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University Cleveland, OH 44106 https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC > On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg > <0000968307750321-dmarc-requ...@jiscmail.ac.uk> 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 lechtenber...@wehi.edu.au <mailto:lechtenber...@wehi.edu.au> > T +61 3 9345 2217 > > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Rhys Grinter > <000022087c81e8c6-dmarc-requ...@jiscmail.ac.uk> > Date: Friday, 10 March 2023 at 12:26 pm > To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > 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 > > > 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/
