[Xplor-nih] Protein collision with PRE data

[Valerie A. Villareal]

Hi everyone.

     I'm calculating the structure of a weak-affinity protein complex
using only PDBs and PRE data. Some of the output structures contain
the two
proteins interlocked or tangled, and sometimes even occupying the same
space. I am using the saWithPreAllNoRdc.py script, in which I
have commented out restraint commands except anything pertaining to
PRE, VDW, RAMA, ANGL, BOND. Any information on why these proteins are
colliding like this? I have also commented out the collapse command.

     Also, will modifying the variables "ini_con = 0.004; fin_con = 4"
help in making VDW repulsion more stringent? For example, changing
fin_con to equal 10 or more? Or are PRE restraints weighted more
heavily when used directly (and not converted to distance restraints)?

 Thanks,
 Valerie