DOT User's Guide |
Version 1.0alpha
|
Released 12/17/1998
|
Release Notes for DOT 1.0alpha
These release notes include information on known problems with DOT
and workarounds.
- The gridstep variable, which specifies the default spacing between
grid points, must be an integer value. There is an issue with rounding
values that will be fixed in the next release. Non-integral values are
treated as an error, and DOT will abort.
- You must be able to use remote shells to use DOT on multiple
computers. Alternatives, such as SSH, do not work. If you have problems
running DOT, check with your system administrator to make sure the
remote shell daemon is enabled.
- On CRAY T3E systems with 128 mbytes per node, you will run out of
memory during the final stages of the run if you compute partition sums.
Edit your command file and set do_partition_sum to 'false'.
-
If the pdb files have a subunit identifier in them, such as "A", it
must be stripped out. Use the UNIX command (shown for the identifier
"A" as an example):
sed "s/ A / /g" input.pdb > output.pdb
- Make sure before running striph that the N-terminal amino acid is
identified as N-term for each atom. For example, VAL should be changed to VALN.
For the C-term, LEU should be changed to LEUC for each atom.
- pdb_to_vol will assign radii to the hydrogen atoms, which shouldn't
have a radius. Thus use a simple awk script to remove all H-atom lines
from the PDB file before running it through pdb_to_vol. Shown below is
an awk command that you may run on the PDB file before running transh:
awk '{ if ($11!="H") printf ("%s\n", $0); }' < file.pdb > file_new.pdb