Hello Taylor-- > > I and trying to use a modified version of refine.py to refine a structure > using > PCS. I modified my script based on a previous post to incorporate PCS using > the > RDC term in the python module. I defined the pseudo atoms for the tensor > parameters in my PDB by incorporating the following lines at the end that I > saved > as a PDB from Numbat: > TER 3055 PRO 291 > ATOM 3056 X ANI 500 -7.594 17.584 17.710 1.00 0.00 LP > ATOM 3057 Y ANI 500 -8.408 17.158 18.785 1.00 0.00 Y > ATOM 3058 Z ANI 500 -7.631 18.334 18.908 1.00 0.00 LP > ATOM 3059 OO ANI 500 -7.439 17.380 18.676 1.00 0.00 O >
We do not generally explicitly set up pseudo atoms input. The helper functions calcTensorOrientation and calcXTensor will configure these automatically. > and I saved my restraint file from Numbat in a format compatible with Xplor: > assign ( resid 500 and name OO ) > ( resid 500 and name Z ) > ( resid 500 and name X ) > ( resid 500 and name Y ) > ( resid 161 and name N ) -1.53600 0.00000 The format is not quite correct: you need to specify one more selection (6 total) corresponding to the paramagnetic center. Perhaps this is at the OO position from above? And please note, that while the four alignment tensor pseudo atom selections are required, they are not actually used in the Python implementation. > Also, I was > wondering what part of the script tells the program to expect a PCS table > instead > of an RDC table? There is no explicit setting. You have configured the energy term to use the distance dependence (1/r^3), and that should be sufficient best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
