Check that all atoms of the 24-atom porphyrin are present in the pdb file. Often, especially with WPDB from shelx, only the asymmetric unit is included.
Fix: import the finished CIF into Mercury and save the isolated porphyrin molecule as pdb.
Make sure that the pdb is consistent with specifications set out at http://www.wwpdb.org/documentation/file-format.php and that atoms are labelled ATOM or HETATM, with C or N assignment.
Fix: Mercury takes care of most of this. Please contact me if you’d like to look at thiaP or similar porphyrinoid structures.
The NSD program doesn’t handle structures with multiple extra-annular nitrogen atoms well, and often fails on this front.
Fix: delete non-porphyrin N-atoms from the PDB file prior to submission.
There is no accounting for disorder in this program – please consider only a single fraction/orientation.
Fix: delete atoms present in minor disorder fractions.
Porphyrins must be submitted separately, as there’s no mechanism for differentiation of structure.
Fix: submit pdbs of each individual porphyrin separately (no need for header blocks).