Hi All Thank You very much for the response and suggestions. I have used Robetta and ITASSER for structure prediction followed by truncating the part according to the rmserror or loop region. However, I was not able to go anywhere after a certain point. R-free is stuck at 40. Even the loop region density is not coming properly. However, I must take a fresh look and get back to you all.
Thank You once agian John On Sun, Jul 4, 2021 at 8:59 AM Randy John Read <rj...@cam.ac.uk> wrote: > Yes, I should have mentioned the truncation by estimated RMS error, which > was part of the protocol we used in the paper with David Baker’s group. > The error estimates are calibrated, I believe, for just the C-alpha atoms, > so they are probably generally underestimates of the errors in the rest of > the atoms in a residue, particularly the side chains; otherwise, the atom > weighting obtained by converting the error estimate into an equivalent > B-factor would be enough to account for errors. > > Randy > > > On 3 Jul 2021, at 17:36, Adam Simpkin <hlasi...@liv.ac.uk> wrote: > > > > I agree that RoseTTAFold would be a good idea! We've been looking at the > models for MR recently and in many cases they're excellent. We've found it > can be useful to truncate the models based on the predicted rms errors with > AMPLE (clearer solutions or even the difference between success & failure) > so this might be a useful strategy to consider if the models don't work in > MR by themselves. > > > > ######################################################################## > > > > 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/ > > ----- > 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/ > ######################################################################## 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/
