Hi Luke, Just reporting to the list what we found out... There were two problems that your case helped me fix: 1. Resolve was reading sequences only up to 132 characters on a line. That is now changed to be unlimited. (The other sequence interpretation tools always read any number of characters on a line, including autobuild/autosol/automr etc). 2. At the end of loop fitting, a check was done to make sure that the new loop does not overlap with anything in the rest of the model. That check was done by reassembling the chains in the model with resolve. It had the side-effect of losing the sequence assignment if the density was poor. The default is now to skip that check (skip_trim=True) in fit_loops, but to carry out the check in autobuilding, reasoning that a user is not likely to try to build a loop where something is already present. These changes are now checked in so versions starting with tomorrow should have the behavior that you were looking for. Thanks for letting me know of the problems! All the best, Tom T
Hi All,
I am trying to see if I can save myself some time by using the loop fitting tools in Phenix. I think I am stalling out because of a trivial problem, but cursory googling, etc, has not helped. Sorry if I should have tried harder. I appreciate any help.
I am using the gui, dev-601. My fasta sequence gets read fine because the output reports the sequence of the missing residues. Whether I use the loop library or not, I get the following error:
Unable to find suitable gap to fill
Then it appears to try to build the loop using sequence from a different chain (I have three chains in my structure).
What am I doing wrong?
Luke
-- Luke M. Rice Assistant Professor and Thomas O. Hicks Scholar in Medical Research Department of Biochemistry, ND10.300 UT Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-8816 phone: (214) 645-5931 email: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb