Dear Longfei,
I am a member of SBGrid Consortium, recently we have two users' bug report about pre 0.7 coot (0.7-pre-1-628), their original post are listed below:
Not sure which version you are referring to, but I assume you meant 3628 (rather than 628).
1) Problem: Torsion angle restraints are no longer functioning in real space refinement. Specifically, torsion angle restraints are turnedon under refinement control, but real space refine is clearly not restraining the rotamers.
Works fine for me (3697). What is the information in the console output? And the traffic lights? You get refinement statistics in the console. If there is no torsion refinement it will be N/A. And the traffic lights for torsion wont be there. In case torsions are used you get a chi2 value and traffic lights.
2) I noticed that the recent COOT version "connects" residues adjacent to gaps in the same chain in C-alphas/Backbone View (e.g. residue 64 then parts of the structure were not modeled and the chain continues with residue 70; in the GUI there is a "long" bond between the two residues). As far as I can see the default version is 0.7-pre-1-628. This was not the case with previous versions.
Again, no problem in 3697. There were some changes to this recently IIRC. Maybe try the latest version...
B
Any idea what is wrong there? Longfei -- *Longfei Wang * Postdoctoral Fellow Harvard Medical School 250 Longwood Ave Boston, MA 02115
-- *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: [email protected]
