Charles: You are right, there are large violations. I'm confused about the values that should be used in the CS and DC tables. Our experimental collaborators have given us a table of the CS values (let's call it Set 1), but another computational collaborator uses the value that is subtracted by the isotropic value, 119.3 ppm for non-Glycine residues (let's call this Set 2. In this table, each value is the corresponding value from Set 1 minus 119.3). It seems strange for me that when Set 1 was used, the structures look OK, but with huge violations for CS; when Set 2 was used, the structure look strange but violations are small. What do you think might be the problem? Do the simulation parameters in refine.py matter much? Is there a script specifically designed for membrane proteins? Thanks a lot. Jian
________________________________________ From: Charles Schwieters [[email protected]] Sent: Monday, June 25, 2012 11:56 AM To: DAI, JIAN Cc: xplor-nih at nmr.cit.nih.gov Subject: Re: [Xplor-nih] Factors that determine the tilt angle of a peptide Hello Jian-- > We are calculating the structure of a membrane peptide with two > helices linked with a loop with PISEMA data (chemical shift, dipolar > coupling) with dihedral angle? hydrogen bond restraints for the > helical part, we also have some distance restraints for atoms from > both helices. > > From PISEMA experiment we expect to get models with the right tilt > angle with respect to the membrane normal (i.e., the z-axis), but we > got models with a variety of tilt angles. For example, we expect to > have a tilt angle of 12 to 17 degrees, but some of the models have > tilt angle that is 26, which is way too large. > I'm wondering what are the factors that determine the tilt angle of > the peptide in XPLOR calculation. Are your restraints well-satisfied? There may be some problem such that there are large violations causing convergence problems. If your PISEMA-based restraints are satisfied, then the tilt angle should be correct. No? best regards-- Charles
