On 3/24/10 10:36 AM, Thomas Evangelidis wrote: > Is it possible to set the distance cutoff between a given atom of the > protein and a subset of atoms in the ligand?
Sure, you can create a pseudoatom which is some function of the subset, e.g. the gravity center, and then create a distance restraint between the given atom and your newly-created pseudoatom. One example is at http://salilab.org/modeller/wiki/Restraints%20on%20pseudo%20atoms
> E.g. in some crystal > structures OG1 of a THR forms an H-bond with O1A of ATP, whereas in > others with O2A. In that case can I force Modeller to keep (THR44:OG1 - > ATP266:O1A <= 3.5+-0.1) OR (THR44:OG1 - ATP266:O2A <= 3.5+-0.1) ?
You could use features.minimal_distance for this rather than the regular features.distance: http://salilab.org/modeller/9v7/manual/node97.html#SECTION001031200000000000...
Ben Webb, Modeller Caretaker