In fact, for non-SBs using the PDB, it is far likelier that they will recognize truncated side chains and thus seek help or know what to do themselves, compared to recognizing incorrectly modeled rotamers (as they won’t be checking electron density likely) and atoms with zero occupancy and B-factors, which could lead to fairly incorrect biological interpretations. Best, Debanu
On Thu, Mar 9, 2023 at 7:55 PM Debanu Das <[email protected]> wrote: > 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 > -- --- 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/
