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.