I found the poll I wrote about earlier. This actually is way older than I had expected (2011). You can see the poll results (which was run by Ed Pozharski) and discussion at the time here in the CCP4BB archive: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html
In brief, the results of 240 respondents were: Delete the atoms 43% Let refinement take care of it by inflating B-factors 41% Set occupancy to zero 12% Other 4% Bernhard From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Debanu Das <debanu....@gmail.com> Date: Friday, 10 March 2023 at 2:56 pm To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] To Trim or Not to To Trim 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 <jxb...@case.edu<mailto:jxb...@case.edu>> 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 <0000968307750321-dmarc-requ...@jiscmail.ac.uk<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Rhys Grinter <000022087c81e8c6-dmarc-requ...@jiscmail.ac.uk<mailto:000022087c81e8c6-dmarc-requ...@jiscmail.ac.uk>> Date: Friday, 10 March 2023 at 12:26 pm To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto: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 -- --- LinkedIn: www.linkedin.com/in/debanudas<http://www.linkedin.com/in/debanudas> Cal Alumni: cal.berkeley.edu/debanudas<http://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 ######################################################################## 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/
