PDB to 3D Restraints

Job name :		label for output files
PDB file :		5MB file size limit
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Reference for stacking restraints:	Laurberg M, Asahara H, Korostelev A, Zhu J , Trakhanov S and Noller HF Structural basis for translation termination on the 70S ribosome Nature , 2008 Aug 14;454(7206):852-7.
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Settings: Criteria and Penalty weighting: These parameters affect how strictly stacked bases or base pairs are identified. If your current model is of low quality, more relaxed parameters may be desired. Stacking parameters max_d_c2plane_stack Maximum allowed distance between center of base A and plane of stacking base B min_d_c2plane_stack Minimum allowed distance between center of base A and plane of stacking base B max_d_c2c_stack Maximum allowed distance between center of base A and center of stacking base B max_ang_n_n_stack Maximum allowed angle between normal vectors of base plane A and plane of stacking base B max_ang_c2c_n Maximum allowed angle between center2center vector of bases AB and normal of stacking base A Base pair parameters overall_cutoff No basepairing if total penalty score above this value hbond_distance Penalty weight on hydrogen bonding distance deviations atom_to_plane Penalty weight on vertical distance differences between bonding atoms and plane of paired base angle_baseplanes Penalty weight on angle between baseplane normal vectors of paired bases score_angle_abcd Penalty weight on flipping orientation hbond_angles_proper Penalty weight on proper hbond angle b-a-a2 and a-b-b2 deviations, of bases A and B in bp. Saenger parameter file: no input will use default parameters Normal run test program with ETRNA
The CNS add-on STACK, facilitates RNA base stacking restraints (yellow) in crystallographic refinement.