On 12/10/2020 6:46 AM, Schreuder, Herman /DE wrote:
Dear Phil, 0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied monomers... It may also be related to a (trigonal??) space group... You probably have already tried it, but phaser has the option to give it already solved molecules and ask it to search for additional molecules. Here I would indeed lower the expected % homology significantly, to crudely compensate for the low occupancy. In contrast to the advice of Dale, I would play around with the % homology to find the value which works best.
It was not my intention to imply that one should not "explore" your problem with multiple interpretations -- Only that you have to adjust your assessment of the significance of the results of those tests.
For example, following MR, where you have varied some small multiple of 6 parameters, you trust the working R factor. After you have "explored" an great number of models by varying thousands of parameters the working R now has to be judged by different criteria. If this change is not made one will be misled to have more confidence in the model than is truly justified. We all agree on this.
This problem, however, is not specific to the working R. If you calculate five kinds of maps and pick the one with the tallest peak at your favorite site, the "sigma" of that peak has to be considered less significant than a peak of equal "sigma" in a map that you decided to calculate before you collected data. (I'll leave my objections to the idea of measuring peaks in "sigma"s for another day.)
When we go hunting in situations like Prof. Jeffrey's our criteria are more squishy. Usually one varies a parameter or chooses a alternative map type based on "interpretivity". All I'm saying is, if you calculate twenty different maps and pick the one that is easiest to interpret, you have to consider the significance of that increase in ease of interpretation to be less than if you defined ahead of time the map you planed to look at.
Yes, when your defined protocol fails, look around for alternatives. Just ensure that your personal skepticism setting is cranked up when doing so.
Dale Tronrud
My 2 cents, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Phil Jeffrey Gesendet: Donnerstag, 10. Dezember 2020 14:49 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Finding partial occupancy monomer by MR ? Preamble: I have an interesting crystal form with 3 monomers (~400aa) at full occupancy and apparently one at much reduced occupancy. It was built recently from Se-SAD and was in moderately good condition: Rfree=32% for trimer, 2.6 Å. In recent refinement cycles it became obvious that there was a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc density that corresponded to a "confusing" set of low-occupancy SeMet sites found by SHELXD and Phaser-EP. The experimental map was bad in that region and was probably flattened during density modification anyway, in retrospect. Question: Phaser failed to find the 4th monomer after trivially finding the other 3 with a recent version of the monomer. I'm wondering if there's a way to indicate "this one is partial occupancy" to Phaser, or if there's a way to improve the odds of success beyond just lowering the expected % homology. Or if anyone has had success with other programs. This is perhaps a rare edge case but I naively expected Phaser to work. In the end I used the weak SeMet sites to locate the monomer and the occupancy appears to be around 0.32 in refinement. Cheers, Phil Jeffrey Princeton ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=G28AUNQrAgQYblmaYBVnXESTXiekmWzfTLPMMX%2B%2BOgw%3D&reserved=0 This message was issued to members of https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WitzjV%2F3hzx1SzMmmDzKVX56uVBD1fXluDDAcyY8Y1g%3D&reserved=0, a mailing list hosted by https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=wv3OjpY8AGsTj0RfiiEMjWPLDD5QOMvfV1TwcaRXczs%3D&reserved=0, terms & conditions are available at https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mEy2Z2rqn8IBmLklgmDe0%2BZOXq4gcLHqSqze6fW%2Fhx4%3D&reserved=0 ######################################################################## 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/
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