Just to repeat the subject, it appears that pymol takes no account of the SCALE records in a PDB file.
The built in assumptions of the orientation of the unit cell therefore gives an erroneous relationship between the unit cell and the atomic co-ordinates. The attached file demonstrates the problem. "Show->Cell" puts the long dimension of the cell perpendicular to the line of the atoms, rather than collinear with them as it ought to be. More seriously then, "symexp" gives a completely wrong expansion. HEADER UNKNOWN TITLE AUTHOR GENERATED BY XX2PDB (Keith Refson, 1998) CRYST1 5.024 5.024 5.024 39.69 39.69 39.69 P 1 SCALE1 0.338511 0.000000 0.072121 0.00000 SCALE2 -0.169255 0.293159 0.072121 0.00000 SCALE3 -0.169255 -0.293159 0.072121 0.00000 HETATM 1 H00 NON A 1 0.000 0.000 6.933 1.00 0.00 H HETATM 2 F00 NON A 1 0.000 0.000 5.792 1.00 0.00 F HETATM 3 F00 NON A 1 0.000 0.000 8.073 1.00 0.00 F HETATM 4 Na00 NON A 1 0.000 0.000 0.000 1.00 0.00 Na TER 4 NON A 1 END sincerely Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 778023 K.Refson@ F: 01235 445720 @rl.ac.uk
