PDB to Restraints
| PDB to 3D Restraints |
PDB to 3D Restraints
Job name :
label for output files
PDB file :
5MB file size limit
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
, 2008 Aug 14;454(7206):852-7.
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.
Maximum allowed distance between center of base A and plane of stacking base B
Minimum allowed distance between center of base A and plane of stacking base B
Maximum allowed distance between center of base A and center of stacking base B
Maximum allowed angle between normal vectors of base plane A and plane of stacking base B
Maximum allowed angle between center2center vector of bases AB and normal of stacking base A
Base pair parameters
No basepairing if total penalty score above this value
Penalty weight on hydrogen bonding distance deviations
Penalty weight on vertical distance differences between bonding atoms and plane of paired base
Penalty weight on angle between baseplane normal vectors of paired bases
Penalty weight on flipping orientation
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
test program with ETRNA
, facilitates RNA base stacking restraints (yellow) in crystallographic refinement.