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Coordinate files and derivative data

When accessing an atom file, a specified filename is tried first. If this is unsuccessful, MODELLER automatically expands the original filename by adding extension '.Z'. This allows it to detect atom files compressed with the UNIX compress command. If the compressed file exists, MODELLER automatically uncompresses it, reads it, and puts it back into the original state after the reading is finished. If the specified file is still not found, the extensions '.atm', '.pdb', '.ent', and '.crd' are tried in this order, without and with extension '.Z', then also with the 'pdb' prefix. This search for the atom file is repeated through all the directories in ATOM_FILES_DIRECTORY (directories are separated by ':'), unless input atom filename starts with '/', in which case ATOM_FILES_DIRECTORY is neglected. Finally, if still unsuccessful and the file specified by the environment variable $PDBENT exists, the coordinate filename (, the 4 character PDB code) is matched to the list of the full PDB filenames in $PDBENT (compressed and uncompressed). For example, $PDBENT file may be:

/disk2/pdb/pdb.pdb.bnl.gov/all_entries/uncompressed_files/pdb1ema.ent
/disk2/pdb/pdb.pdb.bnl.gov/all_entries/uncompressed_files/pdb1hbp.ent
/disk2/pdb/pdb.pdb.bnl.gov/all_entries/uncompressed_files/pdb1gpy.ent
/disk2/pdb/pdb.pdb.bnl.gov/all_entries/uncompressed_files/pdb6gpb.ent
/disk2/pdb/pdb.pdb.bnl.gov/all_entries/uncompressed_files/pdb1fia.ent
etc.

Any derivative data that MODELLER may need, including residue solvent accessibilities, hydrogen bonding information, dihedral angles, residue neighbors, ., are calculated on demand from the atomic coordinates. The most time consuming operation is calculating solvent accessibility, but even this calculation takes less than 1 sec for a 200 residue protein on a Pentium III workstation.

MODELLER stores the filenames of coordinate sets in the alignment arrays. These arrays are used by COMPARE, MAKE_RESTRAINTS, MALIGN3D, ALIGN2D, and several other commands. If these filenames do not change when the structures are needed for the second time, the coordinate files are not re-read because they should already be in memory. This creates a problem only when the contents of a structure file changes since it was last read during the current job.


next up previous contents index
Next: File types Up: File naming Previous: Output.   Contents   Index
Bozidar BJ Jerkovic 2001-12-21