Common Problems

Cannot load pdb: make sure there is only one model in the file; open the structure in PyMOL and save it under a different name. NaN and/or infinity chi2 and/or distances: one or more AV simulations produced empty clouds. Inspect the respective labeling positions, remove the atoms which interfere with the dye linker. After “refinement” some labeling sites can be blocked by other subunits, i.e. having some NaN/Inf structures after refinement is normal. Cannot load pml scripts: usually the problem is that the script refers to the absolute paths of pdb files of the docked units. Open the script in a text editor and make sure that the paths are still valid.