I believe Julia is absolutely right. The other consideration that I haven’t seen mentioned yet in this thread is the effect on refinement. If you truncate a side chain or set it to zero occupancy then the bulk solvent mask would contain that region that is actually occupied by the flexible side chain in the crystal. The solvent mask is supposed to represent flat unordered solvent, and shouldn’t contain such ordered (though flexible) parts of the macromolecule. This is unavoidable in the case of larger unmodelled regions (e.g. missing surface loops, even whole domains at low resolution) and this hard problem is not accounted for using existing tools. But the simpler case of flexible/disordered side chains is something that we can do something to avoid: just build the side chain in and let the B-factors be accordingly inflated - those atoms must be approximately in that position in the crystal due to being restrained by covalent bonding, and the high B-factors will reflect the uncertainty/flexibility of the positioning.
And these days there are sufficient regularisers in use that the additional parameters from explicitly modelling the side chain shouldn’t be a problem, even at low resolution. Having more parameters *should* reduce Rwork if anything… although it will of course depend on refinement protocol/weights etc. Zero occupancy atoms are not physically meaningful, and the fact that they are ignored during refinement means that the B-factors wouldn’t get refined and so wouldn’t reflect positional uncertainty, which could cause further issues with downstream misinterpretation. Similarly partial occupancies shouldn’t be used unless to specifically reflect the modelling assumption that those atoms are only physically present in a portion of the crystal. Regards, Rob > On 10 Mar 2023, at 09:05, Julia Griese <julia.gri...@icm.uu.se> wrote: > > > CAUTION: This email originated from outside of the LMB. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > .-owner-ccp...@jiscmail.ac.uk <mailto:owner-ccp...@jiscmail.ac.uk>-. > > Hi all, > > My impression has been that the most common approach these days is to “let > the B-factors take care of it”, but I might be wrong. Maybe it’s time to run > another poll? > > Personally, I call any other approach R-factor cosmetics. The goal in model > building is not to achieve the lowest possible R-factors, it’s to build the > most physically meaningful, most likely to be correct, model. So if you know > that the side chain is part of the protein, you should model it the best way > you can. If it’s there, just disordered, then the most correct way to model > it is to let it have high B-factors. Most molecular graphics programs don’t > flag zero-occupancy atoms, so the user might never notice. Truncation of a > side chain, unless there is evidence that it really physically isn’t there, > is also misleading, in my opinion. I don’t believe that it is more helpful to > the non-expert user than high B-factors either. > > If people who are not structural biologists themselves don’t know how to use > a structure, then we need to educate them better. It is very straightforward > these days to look at electron density in the PDB viewer. It used to be > difficult, but nowadays there’s no excuse for not checking the electron > density. The PDB validation flags RSRZ outliers. You can easily colour a > structure by B-factors. It doesn’t take that much effort to teach students > how to validate structures. The main point you need to get across is that it > is necessary to do so. And this needs to be done not only in courses aimed at > prospective experimental structural biologists, of course, but whenever > students use structures in any way. > > This is just the opinion of someone who feels very strongly about teaching > structure validation and rejoices when students’ reply to the question “What > was the most important thing you learned today?” is: “Don’t blindly trust > anything.” > > > Cheers > > /Julia > > -- > Dr. Julia Griese > Associate Professor (Docent) > Principal Investigator > Department of Cell and Molecular Biology > Uppsala University > BMC, Box 596 > SE-75124 Uppsala > Sweden > > email: julia.gri...@icm.uu.se <mailto:julia.gri...@icm.uu.se> > phone: +46-(0)18-471 4982 > http://www.icm.uu.se/structural-biology/griese-lab/ > <http://www.icm.uu.se/structural-biology/griese-lab/> > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Bernhard Lechtenberg > <0000968307750321-dmarc-requ...@jiscmail.ac.uk > <mailto:0000968307750321-dmarc-requ...@jiscmail.ac.uk>> > Reply-To: Bernhard Lechtenberg <lechtenber...@wehi.edu.au > <mailto:lechtenber...@wehi.edu.au>> > Date: Friday, March 10, 2023 at 05:07 > To: "CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>" > <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> > Subject: Re: [ccp4bb] To Trim or Not to To Trim > > 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 > <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/ <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 > <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 > <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 > <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 > <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 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen > avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise the > sender and know the content is safe. > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det > att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan > du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > <http://www.uu.se/om-uu/dataskydd-personuppgifter/> > > E-mailing Uppsala University means that we will process your personal data. > For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > <http://www.uu.se/en/about-uu/data-protection-policy> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <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/
