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Re: [modeller_usage] special restrains for aromatic packing interactions

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#SECTION001031200000000000000

	Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
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