Ribbons 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
• 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
• 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
• 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
• dsn6stat --- outputs information about a FRODO map
• elec-tri --- color a surface by electrostatics
• entry-ribbons --- convert *.pdb entry to default display files
• facets --- output contours of FRODO map as *.tri file
• fithelix --- fit alpha carbons to helices
• geom-ps --- converts geometric strain to PostScript plot
• hx-dipole-cyl --- convert pdb-hx-fit output to multi-color cylinders
• hx-mono-cyl --- convert pdb-hx-fit output to mono-color cylinders
• ilabel --- add text to a saved SGI *.rgb image
• interhx --- calculates angles between helices
• ipaste --- display SGI *.rgb image
• iwhite --- change *.rgb file to white background
• luz-ps --- converts Luzzati plot information to PostScript plot
• merge-lists --- used by error analysis protocol
• 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-bbond --- make bond *.cyl file, color by B-factor
• pdb-bond --- make bond *.cyl file
• pdb-chis-ss --- make protein *.ss file from sidechain dihedrals
• 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-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-sele-pdb --- select subset using X-PLOR selection
• pdbext-model --- make *.model file from extents, not center
• polys-data --- GUI to create polygonal surface data
• rama-plot --- display ramachandran plot (not on ESV)
• 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
• ribbon-model --- convert *.pdb file to ribbon model
• ribbons --- ribbon graphics display
• 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-paste --- add 2 rsr fields to an *.ss file
• rsr-ps --- converts real-space R list to PostScript plot
• rsr3-paste --- add 3 rsr fields to an *.ss file
• 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
• 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
• surf-ps --- converts accessible surface list to PostScript plot
• texts-data --- GUI to create text string data
• 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
• O-chi-ss --- convert O sidechain into *.ss field
• O-pep-ss --- convert O peptide plane into *.ss field
• O-rsr-ss --- convert O real space R into *.ss field
• X-bf-ss --- convert X-PLOR B-factor into *.ss field
• X-geom-ss --- convert X-PLOR geometric strain into *.ss field
• X-rms-ss --- convert X-PLOR rms shifts into *.ss field