Just to follow up on this — if you’ve already tried searching for the additional domain with the already placed ones fixed, and that didn’t work, it’s possible that the missing domain is less well-ordered than the ones you’ve already placed. So one thing you could try is increasing the relative B-factor of the new domain you’re searching for, with the SEARCH BFACTOR command in a keyword script, or activating the “Search with bfactor” option in the Expert parameters section of ccp4i. Unfortunately, it looks like this is one of the few options that isn’t yet available from the ccp4i2 interface! I’d probably try a number like 20 A^2 as a guess.
If this doesn’t work, then it’s probably worth cutting out the density and treating it as a real-space MR problem, using the phased translation target at the translation step of the search. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 14 Sep 2020, at 11:27, Schreuder, Herman /DE <[email protected]> > wrote: > > Dear Andy, > > I few thoughts from my side, but no solution I am afraid: > • Your twinning operator -h, -k, l is the standard alternative indexing > for P3x space group, which makes a lot of sense. > • P32 is a low symmetry space group, which makes MR easier, but this is > offset by the NCS. > • In my hands, MR is surprisingly insensitive to twinning, so I would > search for the molecules using the twinned data. Also, for MR one does not > need extremely high resolution data. > • However, twinning and low resolution data seriously hamper “de novo” > model building. So if you have good MR models for your d1 and d2 domains, you > may have a good chance of solving the structure. If you would have to build > them “de novo” in a MR electron density map, you may be doomed. > • What I would do, is to look at the phaser map using a very large map > radius: say 35-40 Å or more and look in the solvent region if there are > places with higher density that may suggest the presence of the missing > domains. If something shows up, you can focus on those regions in your MR, or > even try to manually fit the Ca chain of your MR model. > • You certainly have already done it, but Phaser has to option to > search for additional domains, given the domains you already found. > > Best, > Herman > > > Von: CCP4 bulletin board <[email protected]> Im Auftrag von Andrew > Lovering > Gesendet: Montag, 14. September 2020 11:17 > An: [email protected] > Betreff: [EXTERNAL] Re: [ccp4bb] Best protocols to advance a low resolution > twin > > EXTERNAL : Real sender is [email protected] > > > > To follow on from this thread: > > To answer Jon, I did try to see if P6 subgroups were a possibility but can > rule this out for a few reasons (MR doesn’t give solutions, merging stats not > suggestive of P6, the other dataset with the twin fraction that is > significantly further from 50:50); and the d3:d3 NCS is not parallel to any > crystallographic axis > > The spacegroup is indeed P3 sub 2, not P321, and the solution again only > possible in P3 sub 2 not P3 sub 1, so spacegroup confidence is high > > I did get one reply from Petrus Zwart that twin refinement / map improvement > is a subject being worked on > > What I might try is a Phaser MR where the “missing domains” are searched for > using cut out density of the one placed domain, rather than model (which > could possibly be a better choice at this low resolution? Thoughts > appreciated) > > Best wishes & thanks everyone > Andy > > 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 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/
