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Dear Modeller users, I have two proteins with interacting side chains. I would like to make distance restraints between their Glutamine atoms to ensure that they are a fixed distance apart. To do so I used the following code during optimization: mdl.restraints.add(forms.upper_bound(group=physical.sd_sd_distance, feature=features.distance(a['HE21:2:A'], a['OE1:24:B']), mean=1.9, stdev=0.3)) However, no change has been made to these atoms in the optimized PDB file. Furthermore, the log file shows that all 72 restraints of this type that were applied have violations. It looks as though the program has noted that restraints need to be made, but then does nothing to make these restraints. The only other restraints are: mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False) Thank you in advance for your help, Abdullah Ahmed Windows Live Hotmail: Your friends can get your Facebook updates, right from Hotmail®. |