Hi Jessica, The suggestion by Eleanor and Thierry to break the model into two parts for molecular replacement should work. However, if it doesn’t there’s another option, which can work well in marginal cases. Fix the domain that’s well-placed. Make a note of the Euler angles from the MR solution that placed this domain correctly. Now run a second Phaser job, but this time choose the brute-force rotation function option, and instead of searching all possible orientations just take orientations within, say, 10 degrees of the same set of Euler angles (which will give you similar relative orientations). There won’t be that many orientations, so to avoid missing the best choice turn off rotation clustering and select all of those angles for use in the next step, which is to run the translation searches.
If you were doing this with keyword scripts, the relevant keywords would be TARGET ROT BRUTE ROTATE VOLUME AROUND EULER 10. 20. 30 RANGE 10. PEAKS ROT CLUSTER OFF PEAKS ROT SELECT ALL (at least if the Euler angles for the first domain were 10, 20, 30). However, it shouldn’t be that hard to figure out how to set the same options in the ccp4i or ccp4i2 GUIs. Best wishes, Randy Read > On 24 Mar 2021, at 21:31, Jessica Besaw <jbesaw1...@gmail.com> wrote: > > Hi friends! > > I need advice about the best (or easiest) strategy to refine a piece of an > antibody. > > As seen in the figure below, the right part of the protein fits the density > very well and the left part does not (likely the result of the molecular > replacement model). I can clearly see that the entirety of left domain needs > to be rotated/translated quite a significant amount at a proline residue > (shown as sticks in the middle of the figure). > > What is the best strategy to do this in phenix.refine / coot? Tutorial > suggestions/links would be very helpful. > > <protein.png> > > > Cheers! > > Jessica Besaw > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > <protein.png> ----- 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: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## 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/
