Thanks to Damian for the clear explanation! Just a bit more background. Airlie put this feature in because, with small fragments such as helices (which our collaborator Isabel Usón uses in ARCIMBOLDO), the initial translation function scores are often higher for trials where symmetry-related copies are superimposed, and better solutions were otherwise being excluded because they had much lower scores than these deceptive ones. The advisory is printed out so that the user can be aware this is happening, in case what you need to do (as Damian says) is to go back and edit out a part of your model.
This case turns out to be interesting. Before the structure has been solved, it’s not clear whether the space group is P6522 or its mirror image, P6122. Although P6122 is the answer, P6522 is tested first. In the translation search, there will be peaks where part of the structure is right (the molecules related by the symmetry operators shared by the two space groups) so the likelihood score is much better than random, but the incorrect symmetry will lead to clashes. The advisories come from the translation searches in P6522, and then much better scores without serious clashes are found in P6122. Thanks for sharing the log file so we could see what is going on! 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: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 16 Jun 2020, at 22:40, Damian Ekiert <damian.eki...@ekiertlab.org> wrote: > > Hi Silvia, > > Looking at the end of the log file, it looks like you have a very clear > solution and are ready to go! > > This message means that a better solution from the Fast Translation Function > was excluded because it failed the packing test (too many clashes with > neighboring molecules). Sometimes this will prevent you from getting a usable > solution altogether, and this message would clue you into that. In such a > situation, you could prune flexible/non-conserved loops from your protein and > try MR again with the truncated model. > > But in this case, your still managed to get a very clear solution, so I think > you are ready to look at your maps and begin rebuilding and refinement. > > Good luck! > > Best, > > Damian > >> On Jun 16, 2020, at 4:47 PM, Napolitano Silvia >> <silvia.napolit...@mol.biol.ethz.ch> wrote: >> >> >> Dear ccp44 Bulletin Board, >> >> I am trying to solve a structure by molecular replacement. >> I am doing that by using PhaserMR (simple one-component interface). >> >> I tried out setting up different parameters (e.g.changing # of components, >> #search, different space group search settings...), no matter what I try I >> always get this warning message: >> >> ------------------------------------------------------------------------------------------ >> Advisory: The top solution from a FTF did not pack >> ------------------------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------------------------ >> Advisory: The top solution from a TF rescoring did not pack >> >> (please, see log file attached). >> >> What does this Warning mean? I tried to look it up online but, >> unfortunately, I could not find the answer I was looking for. >> >> Please, let me know if you need more detailed information. >> >> Many thanks in advance for your help and your time! >> >> Best Regards >> >> Silvia >> >> Silvia Napolitano >> ETH Zurich >> Institute of Molecular Biology and Biophysics >> Otto-Stern-Weg 5, HPK E14 >> CH–8093 Zurich >> Phone: +41 44 6332482 >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <MsrAC198-C206_phaser.log> > > ######################################################################## > > 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/
