Programs Developed at HHMI (UMBC): Alphabetical Listing
Alphabetical Listing
- avgsd: calculates
average and standard deviation of a set of numbers.
- best: (OBSOLETE) save the best n
structures from a DIANA calculation.
- byres: sorts DYANA
violations (from overview file) by residue number.
- byviol: sorts DYANA
violations (from overview file) by size of violation.
- calcrms: calculates the average
pairwise rmsd for a family of structures.
- cntres: counts DYANA
restraints of different types.
- cor2pdb: convert
DYANA .cor files to Brookhaven PDB format.
- di2tbl: extract
strong secondary structure NOEs from DYANA limit files.
- drst: (OBSOLETE) graphical
utility to aid in writing DIANA restraint files.
- dsp2pdb: (OBSOLETE)
convert DSPACE .pdb files to Brookhaven or InsightII PDB format.
- extrang: extract one
or more structures from a DIANA .ang file with multiple
structures in it. May be obsolete.
- fit: fits xy data to a
user-specified equation.
- fixpov: fixes the Povray
(.pov) files output by MOLMOL.
- hdr2conv: produce
a script to convert GE Omega .xpt files to NMRPipe format using
information from the Omega .hdr file.
- helixgen: generate
DYANA restraints for ideal helices.
- keepless: (OBSOLETE)
keeps DIANA structures with penalties less than a specified
value.
- limitsrch:
search DYANA limit files for restraints to specific atoms or
residues.
- lisviol: (OBSOLETE)
extract violations from a DIANA .res file.
- mergelists:
merges two or more NMRView lists, removing duplicate entries.
- mk1sup: generates a
Midas macro to superimpose several source structures onto one
destination structure.
- mksup: generates a
Midas macro to do all of the superpositions necessary to
calculate the average pairwise rmsd for a family of structures.
- mksym: creates symmetric
restraints (DYANA format) for dimeric molecules.
- mscript: wrapper around
molscript and raster3d
- mscript.old: same as
mscript, but uses the old version of
molscript.
- mspp: creates molscript input files
from a files with more Midas-like syntax
- mterm: command editing and
terminal I/O for Midas.
- nmrview: wrapper around the "real" nmrview.
Prompts the user to make a backup copy of the .db file. See the
online documentation for nmrview
for the startup options.
- nmrview.old same as
nmrview above, but uses the release last released
version of nmrview before the current one.
- nv3: wrapper around the "real" nv3.
Prompts the user to make a backup copy of the .db file. See the
online documentation for
nv3
for the startup options.
- pklist: fixes labels and
clones and extracts dimensions of an NMRView peak list.
- resviol: (OBSOLETE) predecessor to byviol
and byres. Only works on DIANA .res files.
- rma: summary and statistics
of the results from
quadric_diffusion.
- rstrn_close:
(OBSOLETE) pulls out restraints for residues within a specified
distance in primary sequence. Works with InsightII and DSPACE
restraints.
- splitpdb:
splits up a mulit-model pdb into multiple single-model pdb files.
- stackload: load today's tape for the
system backup on Tuesday through Friday (cobalt only).
- txt2di: (OBSOLETE) takes a text file with
restraint information and formats it for DIANA. Not needed
since DYANA takes free format restraints.
- uplsrch: GUI tool for
searching DYANA limit files for restraints to specific atoms or
residues. It is a graphical front-end to the limitsrch command.