You know there are alternative origins for P43212 - and a different MR search very often will opt for a different origin..
from CCP4 doc P4(123)2(1)2 - I4(1)22 N*origin* Xo Yo Zo 1 0.0000 0.0000 0.0000 2 0.0000 0.0000 0.5000 3 0.5000 0.5000 0.0000 4 0.5000 0.5000 0.5000 Use csymmmatch pdbin new-one.pdb pbin-ref old-one.pdb Or In CCP4I2 - task -Match model to original will suggest which change of origin is needed. On Mon, 6 Sept 2021 at 06:50, Ethan A Merritt <merr...@uw.edu> wrote: > Two questions > > (1) What is the rotation+translation operation that relates > solution #1 an solution #2? > > (2) Have you double-checked and then checked yet again that both > solutions are in P43212? Could it be that one of them ended > up in, say, P414241? > > it's happened to me :-( > Ethan > > > On Sunday, 5 September 2021 21:45:39 PDT Lande Fu wrote: > > Dear all, > > > > > > Recently I had a strange problem related to MR and it confused me and my > colleagues a lot. > > > > My protein crystal was diffracted at 2.63A and I processed it normally > then did MR with Phaser (in P432(1)2). The result itself looked okay and > well fit the map. However, the R-work/ R-free value was stuck at > 0.3012/0.2434 after cycles of manual refinement. Then I redid MR with > another model from PDB website and got another solution which looked > similar to previous one and the R-work/ R-free value can be lowered to > 0.2496/0.1967 after refinement. > > > > Strange things appeared when I opened the two MR solutions in single > coot window (Fig 1). The two models were neither overlaying each other nor > on the symmetry of the other. The two models are nearly identical (actually > the first model was a previous structure built from PDB model) and have > same construct with my protein. There is no TNCS, twinning or other > noticeable problems detected according to aimless log. > > > > My question is: why phaser gives two different solutions from same map > and similar model and result in different R-work/ R-free value? Does that > mean there are two phases in the map? Does that imply multiple lattices in > my crystal? > > > > I tried to research myself but did not find any related explanation for > it. Please let me know if you need more information. Thank you in ahead. > > > > > > Regards, > > > > Lande Fu > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > ######################################################################## > > 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/ > ######################################################################## 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/
