QS knows nothing about most of the PDB identifiers, and can not understand anisotropic B factors. Your PDB file must be as simple as it can be : it should contain a CRYST card (followed by unit cell dimensions and space group number for the target structure) and a series of ATOM cards on the following lines. QS will ignore all lines that do not start with CRYST or ATOM. This means that if you want to include HETATMs in the calculation, you must change HETATM to ATOM in your PDB file. Also note that QS doesn't check the occupancy column, so if your PDB file contains discretely disordered residues, QS will include them in the calculation at full occupancies. Additionally, QS will assign to all atoms of a model the same isotropic temperature factor. If some parts of your models have Bs in the 60Å2 range, you may want to exclude them from the calculation by deleting them from the PDB file. Finally, please note the QS's universe comprise only carbon, nitrogen, oxygen and sulphor atoms. Everything else will be treated as carbon atoms with the exception of (i) phosphorus atoms which will be treated as sulphor atoms, and, (ii) hydrogen atoms which will be ignored. A minimal but functional PDB file could be :
CRYST1 38.070 33.200 46.120 90.00 110.06 90.00 4 ATOM 1 N LYS 1 -7.237 14.795 -10.161 1.00 58.48 ATOM 2 CA LYS 1 -6.682 13.509 -9.562 1.00 57.62 ATOM 3 C LYS 1 -6.904 13.768 -8.083 1.00 49.27 ATOM 4 O LYS 1 -6.436 14.842 -7.821 1.00 46.31 ATOM 5 CB LYS 1 -5.227 13.264 -9.843 1.00 47.34 ATOM 6 CG LYS 1 -4.509 11.995 -9.589 1.00 40.83 ATOM 7 CD LYS 1 -3.472 11.949 -8.511 1.00 42.51 ATOM 8 CE LYS 1 -3.142 10.659 -7.735 1.00 29.40 .................................................................. ATOM 994 OXT LEU 129 9.815 9.083 4.618 1.00 98.99In the risk of becoming repetitious : The CRYST card should be followed by a, b, c,
,
,
and space group number of the target structure.