We dealt with this in-depth during structural genomics days when we deposited over 1500 novel, high-quality, experimentally-phased structures into the PDB. Think it’s prudent to trim/truncate side chains without reliable density.
Non-structural biologists using PDB structures without expert help can err in any of these scenarios: misinterpreting most common/random rotamer, zero occupancy atoms, B-factors, etc. What is the value of populating the PDB, which is a structural model repository, with such information that is not there, i.e., reliable structural model? Any trained crystallographer/structural biologist can easily add in side chain information if needed for modeling/computational chemistry reasons. Best regards, Debanu On Thu, Mar 9, 2023 at 6:50 PM Jurgen Bosch <[email protected]> wrote: > 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 < > [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] > 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 > > ------------------------------ > > 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 > -- --- LinkedIn: www.linkedin.com/in/debanudas Cal Alumni: cal.berkeley.edu/debanudas ######################################################################## 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/
