Hello all, I'm having some issues with crystal contact analysis of a new structure I've solved. I initially tried to get the crystal contact areas using the PISA server on PDBe, but the results did not include several crystal contacts that I had identified myself using COOT. I tried running PISA locally with CCP4 version 6.1.13, but I had the same issue, there were missing crystal contacts. I moved on to areaimol. I ran in DIFFMODE IMOL, first SYMMETRY P1 and second SYMMETRY in my space group (P22121) with keyword TRANS 2. The resulting differences still did not include the same crystal contact surfaces. I tried altering the probe radius and the point density, but that didn't change whether I saw the surface or not. Finally, I went into PyMOL and generated the symmetry mates, included the symmetry mates coordinates in my PDB file, and ran areaimol with DIFFMODE COMPARE between the clean PDB and the PDB with the symmetry mates included. This time, areaimol identified the change in ASA at the residues in the crystal contact. I'm quite confused by this, as it seems that areaimol is not calculating the symmetry mates correctly. The output has the right rotation matrices based on the CRYST1 line in my PDB file. Am I not using DIFFMODE IMOL and SYMMETRY right? My other concern is that I didn't see the crystal contacts in PISA either. Any ideas on diagnostics?
-Phillip Gross
