Auxiliary Programs.

Functional command groupings.

• Graphic Display
• Model Data Preparation
• Sphere Data Preparation
• Cylinder Data Preparation
• Secondary Structure Determination
• Surface Data Preparation
• Error Analysis Execution (deprecated)
• PostScript Plots

Alphabetical command listing.

Command ----- Functionality

• access --- create accessible/molecular surface
• ahelix --- analyze secondary structure from C-alpha only
• atom-model --- convert *.pdb file to ball and stick model
• atoms-data --- GUI to create sphere data
• b-to-vet --- add B-factors to Connolly surface files
• bestfits --- best-fits helices to a range of C-alphas
• bonds-data --- GUI to create cylinder data
• bf-ps --- converts B-factor list to PostScript plot
• cell-box-cyl --- create a unit cell box
• chis-plot --- display sidechain 'rama' plot
• chis-ps --- converts sidechain dihedrals to PostScript plot
• cmc-vet --- calculate approximate *.vet surface file
• compare --- superimposes coordinate sets
• dihe-sig --- used by error analysis protocol
• dsn6stat --- outputs information about a FRODO *.dsn6 map
• entry-ribbons --- convert *.pdb entry to default display files
• elec-vet --- estimate electrostatic potential for Connolly surface files
• facets --- output contours of FRODO *.dsn6 map as *.tri file
• fithelix --- fit alpha carbons to helices
• fix-linux-map --- massage Linux FRODO *.dsn6 map to work with facets
• geom-ps --- converts geometric strain to PostScript plot
• hxfite-cyl --- convert pdb-hx-fit output to cylinders
• ilabel --- add text to a saved *.rgb image (SGI only, deprecated)
• interhx --- calculates angles between helices
• ipaste --- display *.rgb image (SGI only)
• iwhite --- change *.rgb file to white background (SGI only, deprecated)
• luz-ps --- converts Luzzati plot information to PostScript plot
• merge-lists --- used by error analysis protocol
• model-copy --- copy one model to another
• model-data --- GUI to create model file data
• ms --- Connolly's molecular surface
• ms-cyl --- converts *.dot file to *.cyl file
• ms-input --- converts *.sph files to ms input
• ndots-data --- GUI to create dot surface data
• pdb-atom-sph --- make *.sph file, color by atom type
• pdb-bf-sph --- make *.sph file, color by B-factor
• pdb-bf-ss --- add coloring by B-factor to *.ss file
• pdb-bond --- make bond *.cyl file
• pdb-chi-ss --- make protein *.ss file from sidechain dihedrals
• pdb-ell-tri --- fit ellipsoid to *.pdb file
• pdb-geom-pdb --- make C-alpha protein *.pdb file from fit helix locii
• pdb-geom-ss --- make protein *.ss file from differential geometry
• pdb-hb-cyl --- output mainchain H-bonds in *.cyl format
• pdb-hedra-tri --- make metal coordination polyhedra from a *.pdb file
• pdb-hex-ring --- make hexose sugar ring *.tri file
• pdb-hx-fit --- fit ranges of alpha carbons to ideal helices
• pdb-link-ca --- output linked ball-and-stick from Calpha atoms
• pdb-model --- make *.model file
• pdb-nuc-ring --- make nucleic acid base ring *.tri file
• pdb-nuc-ss --- make nucleic acid *.ss file
• pdb-phob-sph --- make *.sph file, color by hydrophobicity
• pdb-pro-ring --- make protein aromatic ring *.tri file
• pdb-pro-ss --- make protein *.ss file
• pdb-rama-ss --- make protein *.ss file from phi/psi
• pdb-range-sph --- make *.sph file, color by residue ranges
• pdb-range-ss --- make *.ss file, color by residue ranges
• pdb-res-sph --- make *.sph file, color by residue type
• pdb-ribo-ring --- make ribose sugar ring *.tri file
• pdb-sele-pdb --- select subset using X-PLOR/CNS-like selection
• pdb-ss-model --- create model from *.pdb and *.ss
• pdb-sss --- make protein *.ss file, add assorted coloring schemes
• pdb-vet --- create Connolly's surfaces if you have MSP.
• polys-data --- GUI to create polygonal surface data
• pov-image --- render POV raytracing data to an image file
• rama-plot --- display ramachandran plot
• rama-ps --- ramachandran plot in PostScript
• recompare --- refines superimposition of coordinate sets
• reform-lists --- used by error analysis protocol
• ribbon-errors --- execute full error analysis protocol (deprecated)
• ribbon-model --- convert *.pdb file to ribbon model
• ribbons --- main graphics display program
• ribbons-data --- GUI to create and manage all ribbons data
• ribbons-demo --- ribbon graphics demonstration script
• ribbons-help --- display hypertext help screens
• ribbons-gallery --- display additional favorite images
• ribbons-image --- display SGI ribbons demo images
• ribns-data --- GUI to create ribbon model data
• rms-ps --- converts rms shift list to PostScript plot
• RSR --- run real-space residual fit analysis
• rsr-ps --- converts real-space R list to PostScript plot
• sig-ps --- converts error sigma lists to PostScript plot
• sph-bond --- make split bonds colored by sphere type
• sph-color-tri --- colors triangles based on nearest sphere
• sph-link --- output linked list of cylinders from spheres
• sph-ms --- make a molecular dot surface from *.sph files
• sph-vet --- make a molecular VET surface from *.sph files
• ss-hx-range --- determine residue ranges of helices from *.ss file
• ss-ps --- create linear SS cartoon in PostScript
• ss-sheet-range --- determine residue ranges of sheets from *.ss file
• stereo-view --- display a pair of left/right *.rgb files (SGI only)
• surf-ps --- converts accessible surface list to PostScript plot
• texts-data --- GUI to create text string data
• tri-a-tri --- splits multi-colored triangles
• tri-sph-tri --- keeps only triangles near sphere set
• turn-class --- analyzes classes of beta-turns
• vet-rib --- convert Connolly's MSP surfaces to ribbons format
• xmapstat --- outputs information about a CNS/Xplor ascii map