UCSF Dock and those errors that you don't understand.

PDB files are an extremely diverse and weird lot. While they have changed a little over the years (new REMARKS yet same computer-readable format) some particularities have no become as common as to be taken into account by all of the software that reads PDB files.

One such example is ANISOU data. Most structures will look like this:

ATOM     26  OE2 GLU A 962     -35.104  28.228 -16.582  1.00 92.60 

An ATOM (numbered 26) that corresponds to Oxigen Epsilon 2 for a GLUtamic residue in position 962. Then, three x,y and z coordinates, a field for occupancy and B-factor. However under certain experimental conditions (and data quality as well as a user/researched decision) structures can be refined with anisotropy and the PDB file will have an extra line like this:

ANISOU   26  OE2 GLU A 962    10361  13047  11777   -905   -242    465       O 
This field contains more information for the same atom, instead of coordinates it contains the tensors used in the ANSOU refinement. The big difference for the structure itself is that the anisotropic refinement reveals a bit about the motion of atoms in the crystal in a more realistic way than the usual isotropic refinement.

Both PyMOL and UCSF Chimera are able to produce very nice renderings of the anisotropy information. However, and this is the reason for this post, some other programs maybe totally unprepared for this info.
Case in point, UCSF DOCK. We were preparing some files to run docking and we ran into a problem using sphgen. Since he program ended with an error message indicating a line of code in the fortran source, one of my students tried to hack the code. However, years of experience using UCSF DOCK led me to think of the input files not the program itself. A session of trouble shooting allows to identify that the source of the problem was two fold:



ANISOU fields
A residue count that exceeded 1000


I manage to renumber the residues so their count stayed below 1000 and using grep I removed all of the ANISOU fields. Then, sphgen worked.
There you go, something else to consider when your software fails.