This list is guaranteed not up to date. It was last updated on June 14 1997.
HELP Gives help about option INFO Gives extensive help about option SHELL Opens a system shell GENOPT Looks at all the other general options END Goes back to the previous menu $.. Execute a shell command directly %.. Executes commands from a different menu !.. Repeat a previous command SCRIPT Executes commands from a script file DOLOG Opens the log-file NOLOG Closes the log-file GO Passes control from the text window to the graphics window FULLST Ends WHAT If execution the neath way HISTOR Show the options you recently executed GRAFIC Brings you to general menu to use the graphics window GRATWO Brings you to menu to do two dimensional graphics GRAEXT Brings you to menu for fancy graphics COLOUR Brings you to menu to colour atoms/residues PLOTIT Brings you to the menu from which to make plots PORNO Brings you to the menu from which to use the sexy graphics options ITMADM Brings you to the menu for the administration of MOL-objects/items LABEL Brings you to the atomic labeling menu SOUP Brings you to soup manipulation menu 3SSP Brings you to the 'superpose on all' menu ACCESS Brings you to menu for accessibility calculations ANACON Brings you in the contact analysis menu BUILD Brings you to the residue building menu CHECK Brings you to the structure validation menu CHIANG Brings you to torsion-angle menu CLUFAM Brings you in the clusters and families menu DGLOOP Brings you to 3d fragment database menu DIGIT Allows you to regenerate coordinates from stereo figures DOSELF Allows you to do WHAT IF management things (write help, etc) DRUG Brings you to the drug-design, docking, FLEXX interface, menu DSSP Brings you to the menu to work with DSSP (or its emulator) ELECTR Brings you to the menu to work with DelPhi (electrostatics) EXTRA Brings you to a menu that does some other funny things HBONDS Brings you in the hydrogen bonds menu HSSP Brings you in the menu to work with HSSP files MAP Brings you to map handling menu NEURAL Brings you to the neural network toy menu NMR Brings you to the NMR menu NOTES Brings you to menu to make notes OTHER Brings you to the yet another menu that does funny things QUALTY Brings you to the quality control menu REFINE Brings you to amino acid refinement menu SCAN3D Activates the realtional protein database module SCNSTS Allows you to do statistics on SCAN3D and DGLOOP groups SEARCH Brings you to menu to search in the soup SELECT Brings you to the menu to select proteins for SCAN3D SEQ3D Brings you to the menu to regenerate the internal database SETPAR Brings you in the menu to change parameters SETVDW Brings you in the Van der Waals radius menu SHAKE Brings you to the menu to build molecules ab-initio SHOENT Brings you to the menu to look at the internal database SPCIAL Brings you to the 'special' menu (undocumented options) SUPPOS Brings you to the superposition menu SYMTRY Brings you to menu to work with symmetry TABLES Brings you in the spread sheet menu WALIGN Brings you to the menu to work with sequences WATER Brings you to menu to work with water molecules XRAY Brings you to the menu with xray options GROMOS Brings you to menu to work with the GROMOS EM/MD program ANATRA Brings you in the trajectory analysis menu ESSDYN Brings you to the essential dynamics menu TRAMOV Brings you to the MD trajectory movie menu CONOLY Brings you to the Connolly software interface menu GRID Brings you to menu to work with Goodford's GRID program START Read crambin from the internal database GETMOL Reads a PDB file GETMLS Reads a series of PDB files DEMOS Start the demonstration option LISTA List atomic information for one residue range LISTAA List atomic information for multiple residue ranges LISTR Lists all residues in the soup LISTRR List the names and numbers of residues SHOPAT Searches for user defined tri-petides APROPO Get writeup in hypertext window MAN-K Search for a keyword in all SHORT helps FIND Finds an option for you if you only know its name SHORT Gives short help about all options in a menu SHORTT Gives short help about all general options NOVICE Activate that HELP will be automatic with every option $ Prefix for operating system commands % Prefix for commands in another than the present menu NEWMOD Activates WHAT IF version 5.0 (bugged) OLDMOD Deactivates version 5.0 ENGLIS Let WHAT IF continue in English DUTCH Let WHAT IF continue in Dutch FRENCH Let WHAT IF continue in French (prompt only...) SPANIS Let WHAT IF continue in Spanish (prompt only...) SETWIF Change an internal program parameter SHOWIF Displays the value of a program parameter MUTATE Mutate one residue MUTZON Mutate all residues into one same residue type MUTSLF Mutates a range of residues to alanine and back to what it was SUGMUT Suggests mutations for a series of residues TRYMUT Tries to optimise the sequence for a structure DEBUMP Debump one residue DEBHBO Debump residues, optimising H-bonds while at it DEBALL Debump multiple residues DEBTRS Debump residues by translations of whole residues IUKKEL Switches on the flag that makes SAVSOU automatic every 10 options > < Prefixes for renaming commands, using renamed commands ! or . Prefix for repetition of an old command MAKSCR Get demo script for ab initio building in present directory TEACH Activates TEACH mode (needed for teaching scripts MYMENU Activates your menu (if you made one) EDT Gets a file in the editor of your choice ANGLE3 Calculates angle between 3 atoms DIST Calculate distance between two atoms DSTOFF Deactivates continuously updates distances in graphics window MINMAX Determine extremes of a residue range SHOCEL Shows all coordinate and map cell dimensions. TIME Shows present date and time CENXYZ Send an centering command to the graphics screen CHESS Play chess with WHAT IF CHOOSE Select predefined ranges for future options NEWRNG De-activates the CHOOSE selected ranges RENUMB Renumber residues TRAROT Translate and rotate residue ranges LSCRIP Run a script over a series of PDB files WAIT Holds execution till the author hits RETURN (meant for scripts) PAUSE Holds execution for a number of seconds BUTON Switch-on one of the 36 buttons at the bottom of the screen BUTOF Switch-off one of the 36 buttons at the bottom of the screen STEREO Toggles stereo on/off ROCK Toggles ROCK on/off SIMPLE Toggles the automatic MOL-object/item administration on/off SMPLON Switches SIMPLE mode on SMPLOF Switches SIMPLE mode off ECHOSC Shows a given text in the text window AUTOON Toggle command logging in script file on AUTOOF Toggle command logging in script file off MODEF X11 only: switch on fast graphics mode MODES X11 only: switch on slabbing MODEC X11 only: switch on depth cueing MODEP X11 only: switch on perspective view LSTOPN List files that WHAT IF has open at this moment PREGMX Go to the GROMACS menu INIALL Restart WHAT IF FOOOOD Show date and time TOGGLI Toggle an ICONFI flag (dont use!) SHOIRF Show all ICONFI flags SHOBUT Shows status of the 36 buttons at bottom of graphics window STYPEA Show type-ahead buffer MOL200 Run the soup-verification and correction procedure SETEDT Allows yo to choose another default editor GRFAIC Alternative spelling for GRAFIC SPECIA Alternative spelling for SPCIAL QUALIT Alternative spelling for QUALTY SIMPEL Alternative spelling for SIMPLE LESS Generally undoes the action of MORE RESET Equivalent to INIGRP or GRPINI (in DGLOOP or SCAN3D) QUIT Keep executing END till the main menu is reached again * * MYMENU module messages * MYOPT1 Executes my first option MYOPT2 Executes my second option * * GROMACS module messages * GMXPAR Enters the GROMACS parameter menu MAKTPB Makes a GROMACS coordinate file and binary topology file MAKBOX Same as MAKTPB, but including solvent/ions GMXFEM Same as MAKBOX + energy minimisation of the system GMXFPR Same as FASTEM + position restrained MD (startup) run GMXFMD Same as FASTPR + continuation MD run CUTOF1 The short range cut-off radius CUTOF2 The long range cut-off radius EMSTPS Number of steps in energy minimisation PRSTPS Number of steps in position restrained MD (startup) MDSTPS Number of steps in continuation MD WRTFRQ Frequency of writing various properties to output file XTCFRQ Frequency of writing trajectory frames to XTC file DELH2O Flag to select whether remote waters should be removed BOXDIS Minimum distance from protein to any edge of box INTLEV Level of interaction FIXPAR Level of position restraining FIXFGM Force of position restraining RESUSE Use external distance restraining file or not BOXLEV Level of box usage * * 3SSP module messages * MAK3SP Creates a 3ssp file SUM3SP Makes a summary of a 3ssp file PARAMS Activates the 3SSP related parameter menu GRA3SP Puts the hit fragments in the movie GRL3SP Puts the hit fragments in a MOL-item GRF3SP Puts one fragment set from one hit in a MOL-item GRD3SP Puts one entire molecule with hits in a MOL-item GRW3SP Puts whole molecules of hits in the movie GRI3SP Interleaves whole molecules and hits in the movie GRM3SP Puts whole molecules of hits in MOL-item * * ACCESS module messages * INIACC Resets solvent accessibilities to zero SHOACC Does some accessibility statistics SETACC Calculates solvent accessibilities INIENV Cleans the environment information VACACC Calculates the accessibility for residue in vacuum ACCDIF Calculate accessibility because of ligand binding ACCTAB Makes a table out of residue accessibilities ACCALA Calculates C-beta accessibility after mutating to alanine ANASRF Analyses buried and accessible surface PARAMS Brings you in the accessibility parameter menu SHOPAR Shows accessibility related parameters SHOENV Shows which molecules are in the environment ACCGRA Puts accessible dot surface at the graphics VDDGRA Puts Van der Waals dot surface at the graphics NEWENV Does the same as INIENV. Needed for compatibility. CLNACC Does the same as INIACC. Needed for compatibility. * * TRAMOV module messages * TRAGRA Puts a trajectory in the movie TRAGRL Puts the entire trajectory in a MOL-item TRA1AT Follow one atom through the trajectory TRASPH Puts a sphere throughout the trajectory in the movie TRAHBO Puts a trajectory plus h-bonds in the movie TRACEN As TRAGRA, but centered on one specified atom TRARIB Makes a spline movie (CPU intensive) USETOT Mark all atoms in the soup for the follow option USEALL Mark all atoms in residues for the follow option USECA Mark all alpha carbons for the follow option USEWAT Add waters to the follow option FOLLOW Follows multiple atoms through the trajectory LOOPER Loops through the movie BNDBND Makes sure that bonds over boundary are not displayed AMBER Swich default trajectory style to Amber PARAMS Brings you in the ANATRA parameter menu * * ANATRA module messages * ANADST Calculate one distance throufg a trajectory ANAHBO Analyse a hydrogen bond during the trajectory ANAVOL Determine the volume ocupied by an atom in a trajectory ANASUS Analyze water protein contacts in a trajectory TRACNT Counts the steps in a trajectory TRARMS Makes a movie of RMS deviations during a movie TRASCR Executes a script file on a trajectory PARAMS Brings you in the ANATRA parameter menu WADINI Initialises the Whatif Analysis of Dynamics options. WADALL Performs a full-check of a trajectory. WADISC Clears the analysis scipt. WADSSC Shows the analysis script made sofar. WADEXE Runs the trajectory analyses described in the script. WADANA Analyzes the TRAGEO results. WADDIS Adds a distance query to the script. WADANG Adds an angle query to the script. WADTRS Adds a torsion angle query to the script. WAD1HB Adds a single hydrogen bond query to the script. WAD1PP Adds a single residue PHI/PSI query to the script. WADGYR Calculates the radius of gyration. WADGRO Gets a coordinate file from the trajectory. WADHST Monitors secondary structure. WADHBO Monitors the total number of backbone hydrogen bonds. WADDIH Monitors the total number of non-allowed phi/psi combinations. WADACC Monitors the total accessibility. WADFLC Calculates B-factors from the trajectory. * * Messages for the BUILD menu * NBLD Adds one residue n-terminal of existing one CBLD Adds one residue c-terminal of existing one INIBLD Start building new molecule CBLDS Adds residues c-terminal of existing one NEWBLD Builds structure from sequence + sec. struc. pred. OPTCYS Optimize cys-cys bridges after NEWBLD FILGAP Dreams up residues to fil a gap DENFIT Optimizes one residue with respect to density DENFTS Optimizes residue range with respect to density SETPOS Puts a secondary structure element at a user given positie PARAMS Brings you to the BUILD parameter menu * * CHECK menu messages * FULCHK Executes ALL know check options. Results as LaTeX file FSTCHK As FULCHK, but uses a file to determine which checks to run ACCCHK Analyses the accessible and buried surface areas ANGCHK Checks bond angles AXACHK Looks for atoms that are near symmetry axes BBCCHK Backbone conformation normality check BMPCHK Looks for too short interatomic distances BNDCHK Checks bond distances BPOCHK Search for buried unsatisfied H-bond donors/acceptors C12CHK Check of chi-1/chi-2 CHICHK Evaluates torsion angles CHNCHK Verifies the chain names CRDCHK Checks for rounded coordinates FLPCHK Looks for potentially flipped peptide planes H2OCHK Does several checks on water positions HNDCHK Looks for atoms with the wrong hand HNQCHK Looks for flips of H, N, and Q residues using H-bonding INOCHK Check inside/outside distribution of residue types MVMCHK Matthews coefficient (Vm) and other cell volume checks NAMCHK Does a nomenclature check NCSCHK Checks non-crystallographic symmetry NEWCHK Throw away the old summary file NQACHK Does new packing quality control OMECHK Verify omega angle distribution PLNCHK Check protein side chain planarity PL2CHK Check atoms connected to aromatic rings for planarity PL3CHK Uncalibrated planarity check for DNA/RNA or protein with H atoms PUCCHK Verifies ring puckering in Proline residues QUACHK Does packing quality control RAMCHK Calculates Ramachandran Z-score ROTCHK Looks if the residues rotamer is normal SYMCHK Checks the symmetry information in a PDB file WGTCHK Atomic occupancy check XBFCHK B-factor checks * * CHIANG module messages * SHOCHI Shows torsion angles EVACHI Evaluates torsion angles SETCHI Sets one torsion angle in one residue RNGCHI Sets one torsion angle in a whole range of residues CYSCHI Calculates torsion angles in cys-cys bridge VOLCHI Calculates chiral volumes * * FAMCLU module messages * INICLU Delete all clusters SETCLU Manually define a cluster of residues SHOCLU Lists all clusters HYDCLU Create a cluster of buried hydrophobic residues INIFAM Delete all families SHOFAM Lists all families SETFAM Create a family DELFAM Delete a family * * COLOUR module messages * COLATM Set default atom colours COLTYP Colour residues of certain type(s) COLBFT Colour atoms by B-factor COLFAM Colour whole families COLCLU Colour whole clusters COLETM Colour atoms by energy term COLHST Colour residues by secondary structure COLPRP Colour residues by property COLROW Colour by parameter correlation row COLATV Colour by atomic value COLSPC Colour residues according to predefined schemes COLREF Colour residues as function of geometric errors COLBB Colours the backbone COLMOL Colours one molecule COLH2O Colours all waters COLRNG Set the extremes of colour ranges COLZON Colour one range of residues COLZNS Colour zones of residues COLACC Colour as function of accessibility COLABF Colour by residue averaged B-factor COLTAB Colour residues as function of a table value COLSCH Colours side chains COLBIN Divides colours over equally populated bins COLHSP Colour as function of variability in HSSP file COLSMC Colour as function of symmetry contacts in crystal COLREP Replaces one colour in the soup by another COLSHF Shift a range of colours * * ANACON module messages * CONRES Makes the contact matrix for residues RSCACA As CONRES, but based on alpha carbon distance RSCBCB As RSCACA, but based on beta carbon distance CONATM Makes the contact matrix for residues and atoms CONHAN Makes residue contact matrix coloured by hand CNTRES Counts residue contacts CNTATM Counts atomic contacts LSTATC List all contacts for one atom SHOSBR Show salt bridges SHOPAR Shows the parameters relevant for this module PARAMS (Re-)sets the parameters relevant for this module CONTPS Draws + lists all contacts between types of residues CONTYP Draws + lists all contacts between types of residues CONTAC Lists all interatomic contacts CONDBL As CONTAC but list contacts in both directions BUMPS Lists all atomic bumps BMPTAB Make a table of all bumps * * DGLOOP module messages * DGFIND Finds matching fragments. No constraints DGFIX Finds matching fragments with same central residue DGMUT As DGFIX, but with mutated central residue DGREP After DGMUT, DGREP puts new residue in the soup DGINS Finds loops that can be inserted, backbone only DGINSS As DGINS, but with sequence constraints GRPSHO Show all groups presently available DGSHOW List the hits at the terminal PARAMS Menu to change DG*** parameters RESPAR Resets DG*** parameters TIGHT Tightens DG*** parameters RELAX Relaxes DG*** parameters SHOPAR Shows DG*** parameters GRPINI Re-initiates all groups LENSET Re-sets the length of the groups DGRN-N Finds rotamers for all types at many positions DGR1-N Finds rotamers for one type at many positions DGRN-1 Finds rotamers all types at one position DGRSLF Executes DGR1-1 over a range of residues DGROTA Finds rotamers for one type at one position (=DGR1-1) DGRS-N Displays best rotamer at range of positions DGGRA Puts hits in the movie DGGRAL Puts hits in a MOL-item ALTOCA Converts complete residues into just alpha carbons CATOAL Converts alpha carbons into residues DGR1-1 Finds rotamers for one type at one position (=DGR1-1) * * 2D-3D module messages * DIGPBM Reads PBM file (scanned stereo image of protein) DIGPGM Reads PGM file (scanned stereo image of protein) DIGXFI Read Xfig digitized output DIGGRA Display digitized PBM file DIGSHO Show digit parameters DIGRAT Set ratio between 2D and 3D constraints for optimizing DIGC12 Set optimal distance between adjacent Ca atoms DIGC13 Set minimal distance between 1-3 Ca atoms DIGSTA Set stereo angle used by DIG2T3 DIGNRS Set number of residues to be refined at the same time DIGLWI Set line width used for integration DIGSCL Select scale parameters for refinement DIG2T3 Reconstruct initial 3D from 2D coordinates DIGOPT Optimise 3D coordinates with 2D and 3D restraints DIGTGT Tighten 3D restraints on Ca-Ca distances DIGREL Relax 3D restraints on Ca-Ca distances DIGSH2 Show current 2D coordinates in the XFIG coordinate system DIGPDB Write 3D coordinates to a PDB file * * DOSELF module messages * CHKMES Translates/corrects Dutch lines in MESSAGES.TXT COUNTR Counts source code statistics over WHAT IF modules DOCUWI Put text for placeholders in a WHAT IF source module PRETTY Prints a WHAT IF source module nicely readable RUNOFF Emulates RUNOFF for one chapter of the writeup RUNALL As RUNOFF but for many chapters SEEWPL Lists a MOL-item formatted at the terminal TEXALL As for RUNALL, but produces also TEX output TEXONE As for TEXALL, but now for only one RUNOFF file WIFPAR Checks which WIFPARs are used, and how often DOCDON Lists subroutines that are not yet in chap83 * * DRUG module messages * GETCSD Read a drug from a CSD type file GETML2 Read a drug from a TRIPOS MOL2 file DRGTOP Make a topology entry for a drug WIDOCK Dock a drug, using the WHAT IF dock algorithm DCKOPT Localised drug docking, using the WHAT IF dock algorithm MANDCK Manually dock a drug, with continuous energy monitoring LIGIN Dock a rigid small molecule using Sobolev's algoritm INIFLX Initialize some flex files (cavity file, etc). Interactive. ANIFLX Initialize some flex files (cavity file, etc). Automatic. FLEXX Dock a flexible small molecule using FLEXX INIDDB DOCKDB gets started (should be done first, but only once) SUBSTR DOCKDB Substructure search via smiles-code SUBFRA DOCKDB Substructure search via fragment name FNDCAA DOCKDB Find pairs of contacting residues FNDPDB DOCKDB Find (and display) a PDB file LSTDDB DOCKDB List of searchable PDB files GETFLX DOCKDB Initialize for DOCKDB usage of FLEXX GETDDB DOCKDB Load file from database FNDCPX DOCKDB Demonstration command DDBVQL DOCKDB interactive VQL query * * ESSDYN module messages * WEDALL Performs a full automatic ED analysis WEDTRA Reads trajectory files, creates 1 fitted trajectory file WEDEIG Constructs & diagonalizes covariance matrix WEDPRJ Projects trajectory onto eigenvectors ANWTRA Analyzes WEDTRA output ANWEIG Analyzes WEDEIG output ANWPRJ Analyzes WEDPRJ output PRNSEL Flag to select output (screen/printer) WEDSEL Parameter: determines which atoms should be used for ED SELMAS Fitting with center of mass vs. geometrical center * * EXTRA module messages * FOLD01 determines accessibility change upon local folding FOLD02 determines accessibility change upon global folding FOLD03 makes a pairwise accessibility reduction matrix RANDOM randomizes atomic coordinates a little bit RANALL totally rondomizes atomic coordinates FLDCON makes a window vs outside-window contact plot HELANG determines angle between two helices HELANS determines all inter helical angles in a molecule HLANDB determines all inter helical angles in the database * * GRAFIC module messages * SHOALL Displays all residues. SHOTOT Displays all residues, drugs and waters. ZONES Shows zones of residues, drugs or waters. SPHERE Puts a sphere from the soup in a MOL-item. GRACA Draws a alpha carbon tracing. GRABB Draws backbone (plus beta carbon) tracing. GRASCH Draws side chains. CASCH Combines GRACA and GRASCH. SPHZON Combines SPHERE and ZONES (for one zone). GRAACC Creates an accessible dot surface. GRAVDD Creates a Van der Waals surface. SPLINE Creates a spline (=smooth ribbon with arrows and cylinders). POTH2O Draws potential waters around an amino acid. GRASBR Draws salt bridges. GRACLU Draws one cluster. CROSS Toggle between diverging and cross-eye stereo. ACON Sets the center of graphics at an alpha carbon. LINEWI Changes the linewidth (SG only) CENTER Centers the graphics on the center of the soup. NOMODL Switches the working model off. TOGGL2 Makes two MOL-objects flash alternatingly. OPTVIE Changes the coordinates in soup such that SHOALL is optimal SETVIE Allows interactive setting of some viewing parameters. SHOVIE Displays the most crucial viewing parameters. DIRECT Toggles the direct graphics mode on/off. UNDISP In direct mode only: removes residues from screen. DSHBND Toggles dashed bond mode on/off. DBLBND Toggles double bond mode on/off. INIGRA Deletes all MOL-items and MOL-objects. INIOBJ Deletes one MOL-object. ROTY+6 Rotates the whole screen +6 degrees around the Y axis. ROTY-6 Rotates the whole screen -6 degrees around the Y axis. XONLY Allows for rotations around X only. YONLY Allows for rotations around Y only. ZONLY Allows for rotations around Z only. NOONLY Disables XONLY, YONLY, and ZONLY. HYDON Display hydrogens if available. HYDOFF Never display hydrogens. DEMO10 Mainly for scripts, do a 10 seconds demo ALLGRA Same as SHOALL GRAALL Same as SHOALL GRAPHI Same as GRAFIC GRAPOT Same as POTH2O GRASS Same as GRASCH SS Same as GRASCH GRATOT Same as SHOTOT TOTGRA Same as SHOTOT ROTY6 Same as ROTY+6 VIEWOP Dame as OPTVIE ZONE Does ZONES, but only on one range INIT Same as INIOBJ (INIT -1 does INIGRA) * * GRATWO module messages * PHIPSI Makes phi-psi plot RAMAON Switch on continuously updated Ramachandran plot RAMAOF Switch off continuously updated Ramachandran plot PRPMOM Makes a property plot BFPLOT Makes a B-factor plot ETPLOT Makes a energy term plot PPPSRI Create phi-psi plot in Shrinivasan style ATMLAB Writes text next to atom L2DTYP Labels residues of a certain type in phi-psi plot NOPIC2 Make MOL-items made in GRATWO unpickable PARAMS Activates parameter modification menu * * GRAEXT module messages * AXIS Draws a small axis system in 3 dimensions ARROW Draws a small straigth arrow BARROW Draws a small 90 degrees bend arrow TARROW Draws a small 180 degrees bend arrow CATSCP Draws Calpha tracing + lines indicating contacting sidechains CONCHG Draw contacts to basic and acidic amino acids CELL Draws a wires frame of the crystallographic cell CELLS Draws a wires frame of multiple crystallographic cells DOTATM Makes a dot sphere around one atom GRAAA Draws all residues of (a) certain type(s) in a range GRAAAS Draws all sidechains of (a) certain type(s) in a range HELCYL Draws one cylinder through one helix HELLIN Draws cylinders through all helices HELCA Draws cylinders through all helices + rest in Calpha trace LINATM Draws a line between two atoms PLANET Draws the 'best fitting' ellipsoid around a range PLUTO Draws a residu (drug) range as ball and stick model PLUTOS As PLUTO, but only for sidechains of residues PLUTOP As PLUTO, but sphere will not be dotted but 'lined' BPLANE Draw peptide planes and indicate angles with B0 axis (NMR option) ALLFIL Reads the line/dot/cross/label file DOTFIL Reads dots from a file and displays LOOPCA Loops over database range and make movie of alpha carbon drawings LOOPSP As LOOPCA, but draws whole molecules LOOPST Loops over database and plot SPLINEs of entries (takes hours) SPLPST Very complicate ultra fancy plotting option (try it) SPLPSL Very complicate ultra fancy plotting option (try it) SPLPS+ Very complicate ultra fancy plotting option (try it) LINFIL Reads lines from a file and displays them COLTST Draws a colour circle that shows all full colours ICOATM Draws an icosahedron around one atoms * * ELECTR module messages * RUNDEL Runs the DELPHI program GETODM Reads the electrostatics map made by RUNDEL GETFDM Reads a formatted Delphi electrostatics map from bugnest GETUDM Reads an unformatted DelPhi electrostatics map from bugnest GETUUM Reads an unformatted UHBD/GRID electrostatics map STAELM Does statistics on the default map SCAELM Scales the default map AVG and SDEV according to another map GRDELM Calculates the first derivative of the default electrostatic map HISELM Makes a histogram of a map INVELM Inverts the default map JENS80 Does something too JENS90 Does something too MAKMAP Makes two small maps (for testing purposes) OUTER Remove convex points but keep amost concave ones REMOVE Remove the shell + tunnels into the molecule URANGE Truncates the map between user given limits SMOOTH Smooths the map. (Local moving average) CONVEX Removes convex surface points PEELIT Peels one layer of the shell KPSHEL Puts all 100's at zero KILISL Remove points with only one non-zero neighbour LINER Make the cut through the protein gausian FLATEN Puts all values above a limit at that limit AVER0 Adds a constant to make the average map value 0 INV50 Puts x (for x>50) at 100-x CNT100 Gives statistics about the environment of 100's SPIKER Removes spikes from a map PEEL Removes the entire outer shell MAPAND Sets all points to 0 that are 0 in second map MAPDIF Subtracts two maps SCALER Scales all points between 0 and 100 DEFMAP Changes the default map * * GRID module messages * MAKGRN Prepares default GRIN input file EDTGRN Edits GRIN input file RUNGRN Runs GRIN input file LSTGRN Shows GRIN output at terminal MAKGRD Prepares default GRID input file EDTGRD Edits GRID input file RUNGRD Runs GRID input file LSTGRD Shows GRID output at terminal SETBOX Resets the limits of the GRID map GETGRD Reads in a GRID result map * * GROMOS module messages * MAKGRO Writes a GROMOS file WREGRO Executes WHAT IF's protein-pre-GROMOS option WRUNEM Executes energy minimization automatically HEATUP Runs MD in water using DvA's heat up protocol WRUNMD Executes molecular dynamics automatically CONTMD Start an MD continuation run GETETM Executes energy analysis program PARAMS Brings you to the GROMOS parameter menu ENERAN Does an energy analysis FASTEM No-nonsense fast EM, starting from soup FASTHT No-nonsense fast HEATUP, starting from soup FASTMD No-nonsense fast MD, starting from soup EDITOP Converts any binary topology to ASCII, allowing user modification TRSFIL Produces a phi-psi-omega contraint file for GROMOS MRGTOP Merges two topology files SHOGMT Shows results of last PROGMT run SHOGCH Shows results of last PROGCH run SHOGWH Shows results of last PROGWH run SHOBOX Shows results of last PROBOX run SHOION Shows results of last PROION run SHOEM Shows results of last PROEM run SHOMD Shows results of last PROMD run SHOMMT Shows results of last PROMMT run * * HBONDS module messages * SHOHBO Give hydrogen bonds between two ranges SLFHBO Looks for intra residue hydrogen bonds only GRAHYD Puts hydrogens in a MOL-item ONEHBO Checks one potential hydrogen bond 1ATHBO Find all hydrogen bonds for one atom 1AAHBO Find all hydrogen bonds for one residue HSTHBO Find backbone hydrogen bonds for secondary structure FILHBO Find hydrogen bonds for atom pairs read from file BSSHBO Find hydrogen bonds as function of main/side chain SPHHBO Find all hydrogen bonds within a sphere INIPAR Put parameters back to their defaults SHOPAR Show hydrogen bond related parameters PARAMS (Re-)set hydrogen bond related parameters HB2AWB Add a hydrogen bond to the list of preferred hydrogen bonds HB2CWB Clear the list of wanted hydrogen bonds HB2NET Find the best hydrogen bond network HB2MAK Create a PDB file including the polar hydrogen bonds HB2INI (Re-)initialize the hydrogen bonding module HB2RES Reset all coordinates and forget all H positions. HB2SPN Set the penalty for a flip HB2GRA Show hydrogen bonds between two ranges HB2LIS List all hydrogen bonds HB2LFR List flipped residues and unusual groups. HB2LBF List bifurcated hydrogen bonds HB2LUA List unsatisfied acceptors HB2LUH List unsatisfied donors HB2LPA List all potential acceptors for all donors HB2LAD List all affected donors for each ambiguity HB2XST Extra statistics about the hydrogen bonds HB2ENE Calculate total H-bond energy for a range BBSHBO Doet hetzelfde als BSSHBO HBOBBS Doet hetzelfde als BSSHBO * * HYDRO module messages * SETPRP Set moment calculation type CLCMOM Calculate moments VECMOM Calculate vector moments SHOPAR Show present parameters PARAMS Brings you in the moment calculation parameter menu * * HSSP module messages * SHOHSP Show (parts of) a HSSP file GETHSP Puts variability in property (PRP) array PIRHSP Creates all PIR files from a HSSP file BLDFST Builds structures from a HSSP file fast BLDONE Models the first sequence on the first structure BLDHSP Builds structures from a HSSP file slow GRAHSP Displays the BLDHSP or BLDFST structures as movie VARHSP Displays and plots the sequence variability * * ITEMS module messages * ITMON Switches a MOL-item on ITMOF Switches a MOL-item off OBJON Switches a MOL-object on OBJOFF Switches a MOL-object off DELITM Deletes a MOL-item OBJINI Deletes an entire MOL-object LSTITM Lists all MOL-items MOVITM Puts a MOL-item in FBRT APLSOU Applies MOVITM matrix to part of the soup GRAINI Removes all MOL-objects GETITM Retrieves one old MOL-item GETITS Retrieves multiple old MOL-items MAKITM Writes a MOL-item as a formatted file MODLOF Deletes the working model ITEMON Old spelling for ITMON ITEMOF Old spelling for ITMOF * * LABEL module messages * PCKRES Labels one alpha carbon with residue name/number PCKATM Labels one atom with its type and residue number PCKRNG As PCKRES, but for a range of residues PCKTXT As PCKRES, but asks for the text for the pick label PCKTYP As PCKRNG, but only labels certain types PCKINI Removes all labels PCKLIM Sets a residue range outside which on cannot pick SHOPCK List the labels made with a PCK command or by picking MOVPCK Allows to translate labels, and alter their colour LABRES Puts text label in a MOL-item near an alpha carbon LABATM Puts a text label in a MOL-item near any atom LABRNG As LABRES, but puts the same label at a range PCK1LC Labels a range of residues in 1-letter code INI1LC Removes the PCK1LC labels from the screen * * MAKDB module messages * MAKFMT Creates a formatted coordinate file (ALCOOR.FMT) MAKXYZ Regenerates ALCOOR.XYZ database coordinates from formatted file PRPCHK Checkes if all PDB files required for database generation exist PRP001 Corrects all PDB files (Easily takes 24 hours and 100M space) PRP002 Creates MUTDB.IND and TOTALS.SEQ PRP003 Creates ALCOOR.XYZ (all PDB coordinates) PRP004 Corrects atom correctness flags in ALCOOR.XYZ PRP005 Create ALLHST.HST (secondary structure database by DSSP) PRP006 Create DGloop pointer files PRP007 Puts accessibilities in ALCOOR.XYZ PRP008 Creates the NEACON file PRP009 Creates phi-psi value tables for database PRP010 Creates accessibility tables for database PRP011 Creates atomic contact tables for database PRP012 Creates hydrophobic moment tables for database PRP013 Creates cys-cys bridge info tables for database PRP014 Does nothing PRP015 Puts the eighth torsion angles as term 10 in alcoor PRP016 Makes the secondary structure element tables PRP017 Does nothing PRP018 Creates ALLDSP.DSP for use of original DSSP values PRP019 Creates HSSP derived sequence profiles PRP020 Creates conservation table PRP021 Creates backbone hydrogen bond table AUX001 Creates RAMA.LIN (backdrop for Ramachandran plots) AUX002 Calibrates Ramachandran Z-score (parameters in PARAMS.FIG) AUX003 Calibrates chi-1/chi-2 Z-score (parameters in PARAM.FIG) AUX004 Creates NQA boxes (needs PRP001 and 200M space in current directory) AUX005 Creates NQA residue calibration AUX006 Creates NQA structure calibration AUX007 Creates NQA virtual atom boxes AUX008 Creates inside/outside calibration database (INOUTF.DAT) AUX009 Creates Backbone conformation Z-score calibration AUX010 Creates EVACHI.CHI (Calibration table for CHICHK) AUX011 Creates IMPROPER.DAT (Calibration table for HNDCHK) PRP101 Copy all PDB files to default directory PRP102 regenerate PDB.LIST from the database PRP103 checks if all HSSP files exist PRP107 creates formatted HSSP derived files PRP108 re-creates real HSSP derived files PRP110 Creates the 1-3 bond table PRP115 Creates the 1-2-3 angle table for the soup * * MAP messages * GETMFF Reads an MFF style map into WHAT IF MAKMFF Writes an MFF style map to disk GETFMP Reads a formatted map MAKFMP Writes a formatted map GETXPF Reads a formatted XPLOR map SAVMAP Saves all present map parameters in a file RESMAP Restores all present map parameters from a file SHOMAP Inspect map-related parameters and grid values DEFMAP Changes the default map DELMAP Removes a map from WHAT IF's memory INIMAP Removes all maps from WHAT IF's memory PRBRAD (Re-)set the probe radius for cavity calculations RESOLU Set upper limit on resolution PARMAP Change map-related parameters SRFMAP Creates an accessible surface contour map CAVITY Creates an electron density map for cavities CAVVOL Interactive cavity volume calculation AACAVI Shows residues that touch cavities SMLCAV Calculates local cavity more precise CONMAP Calculates map that represent contacts between subunits RELCAV Makes that more/wider caves are kept TGHCAV Makes that fewer/narrower caves are kept GRAMAP Sends contours to the graphics window GRACOL As GRAFST, but with coloured lines GRAXYZ As GRAMAP, but contours only in one direction AXMAP Puts axes along the shown map fragment * * MAPCON module messages (complete) * MAKCON Creates files needed to run Connolly's program RUNCON Runs Connolly's program LSTCON Get PQMS or TRB related files in the editor DOTCON Makes a dot surface LINCON Displays surface as lines TRICON Displays surface as triangles SOLCON Makes a solid rendered surface shell PARAMS Brings you to the Connolly interface parameter menu * * MAPEDT module messages (complete) * GETENV Reads an envelop into the main map GRAMPP Activates the interactive editing option FIX0 Switch from toggle picking to fixed 0 setting FIX1 Switch from toggle picking to fixed 1 setting NOTFIX Switch (back) to toggling upon picking * * MASMAP related messages * OUTER Remove convex points but keep amost concave ones REMOVE Remove the shell + tunnels into the molecule RANGE Scales the map between 0 and 100 URANGE Truncates the map between user given limits SMOOTH Smooths the map. (Local moving average) CONVEX Removes convex surface points PEELIT Peels one layer of the shell KPSHEL Puts all 100's at zero KILISL Remove points with only one non-zero neighbour LINER Make the cut through the protein gausian FLATEN Puts all values above a limit at that limit AVER0 Adds a constant to make the average map value 0 DENMAP Display density values at the terminal INV50 Puts x (for x>50) at 100-x HISTOG Gives a histogram of density values CNT100 Gives statistics about the environment of 100's SPIKER Removes spikes from a map PEEL Removes the entire outer shell UPDATE Writes a new internal copy to disk MAPAND Sets all points to 0 that are 0 in second map MAPDIF Subtracts two maps SCALER Scales all points between 0 and 100 DUMMY1 Empty option for users to program DUMMY2 Empty option for users to program DUMMY3 Empty option for users to program DUMMY4 Empty option for users to program DUMMY5 Empty option for users to program DUMMY6 Empty option for users to program DUMMY7 Empty option for users to program DUMMY8 Empty option for users to program * * MDF module messages * GETMDF Reads an MDF LSTMDF Lists reflections at the terminal WSTMDF Creates a Wilson plot for one column LCNMDF Lists the column numbers DSTMDF Give statistics on the difference of two columns SBNMDF Sets bin boundaries for COLBIN GRAMDF Puts the requested dots at the screen TALMDF Switches all reflections on TSZMDF Switches refs on as function of size TDFMDF Switches refs on as function of difference TASMDF Switches refs on as function of absency TAAMDF Trigger as function of resolution HKLMDF Trigger blocks of H K L RN2MDF Switches refs off if not in two columns CAKMDF Give all refs one colour CSZMDF Colour refs as function of their size CDFMDF Colour as function of two columns difference CBNMDF Colour per size bin CASMDF Colour as function of absent/present * * MOL module messages * SHOSOU Shows the contents of the soup. INISOU Initializes the entire soup (irreversably). DELMOL Deletes one molecule from the soup. DELMLS Deletes a range of molecules. MAKMOL Writes (part of) the soup to a PDB-file. MAKMLR As MAKMOL, but writes only atoms that are TRUE in a ROW GETGRO Reads coordinates from a GROMOS coordinate file. GETKIN Reads coordinates from a KINEMAGE coordinate file. MAKDNA Creates a DNA molecule. SAVSOU Saves the coordinates, etc. in a save-file. RESSOU Restores the coordinates, etc. from a save-file. SAVSTA Saves the status in a save-file. RESSTA Restores the status from a save-file. DELETE Deletes one residue from the soup. SOUCOP Appends a copy of part of the soup after the last protein. NEWUNQ Renumbers unique identifiers GETDBF Reads a protein from the internal database. PASTE Allows to paste molecules together. CUT Undo a PASTE, or set a CUT flag. PASTAL Pastes everything that can be pasted. INIPAS Clears all previously set PASTE and CUT flags. SHOPAS Shows all PASTEs and CUTs set. SAVAA Saves one amino acid in a residue file. RESAA Restores one amino acid from a residue file. CORAA Corrects a range of residues (where needed). CORALL Corrects all amino acids in the soup (if needed). SETCHA Gives residues a (new) chain identifier. CNTBAD Counts good and bad residues in all molecules. ADDOXT Adds second oxygen to C-terminal residue SHOCYS Shows how many cysteines are paired/unpaired. SETCYS Forces WHAT IF to think that two Cys-es are paired. INICYS Undoes all forced cys-cys pairs. DVADOM Mark all atoms as OK, even if they are not GETUS3 Read PDB files with extended residue names. STATUS Debug option to list soup pointers. CLNSOU Removes overlapping proteins and non-protein from the soup. INVERT Inverts a sequence and adds the new sequence at end of soup MERGED Merges multiple drugs into 1 drug DELDNA Deletes a base pair from two DNA strands HBODNA Lists DNA pairing, based on hbonds pattern SHEARD Lets proteins crawl along DNA NOBOTO Removes connections between residues and other shit FIXDNA Runs a couple corrections on DNA with bad nomenclature SHOTOP Shows the contents of the presently used topology file PASRNG Run PASTE over a range * * NEURAL module messages (complete) * SHOPAR Show the network architecture parameters ININEU Re-initialize all neurons/junctions GETSET Reads teaching and/or testing sets from file SHONEU Display neuron values at terminal SHOSET Shows data set with measured and predicted output NETWRK Allows you to define the network architecture MAKNEU Writes neuron (junction) values in a file GETNEU Reads neuron (junction) values from a file TRAIN Executes training run(s) for the network COOLNW Reduce the 'temperature' of the neurons HEATNW Increase the 'temperature' of the neurons QQSAR Does a quasi-QSAR linear optimization JKNIFE Runs a Jack-Knife training procedure SAVNEU Save network in a file RESNEU Restore network from a file SHAKEN Shake up the net when stuck in local minimum DEBUG Don't use. For programmers only EXAMPL Needed to run the example given in the writeup MAKTST Makes a small test input file for secondary structure prediction SCATER makes a three dimensional scatter plot of simple net results PARAMS Brings you to the parameter menu * * NMR module messages (complete) * USEMLS (Re-)define the molecules to be used LSTMLS List which molecules were selected with USEMLS SUPMLS Superpose all molecules to be used CHKMLS Checks if a the molecules are covalently identical GETDIA reads coordinates from a DIANA file MOTMLS Does a MOTIF based superposition of multiple structures CAMLS Display alpha carbon trace of molecules to be used ZONMLS Displays one zone from all molecules to be used BBBALL Display backbone in (small-)ball and stick mode GRABBD As BBBALL, but without H's atoms PEPLAN Display peptide planes VECPLN Display peptide planes, and the angles with B-zero NMRHND Makes plot at graphics screen of residue handedness TOPOLO Reads a new topology file AVRMOL Averages molecules * * NOTES module messages (complete) * AANEW Initializes the notebook for a residue AANOTE Adds a note in the notebook for a residue AASHOW Shows the contents of the notebook for a residue MAKNEW Create a new general notebook USEOLD (Re-)open an existing general notebook WRITE Write a note in the general notebook NINDEX Show the index of the general notebook PRINT Print (part of) the notebook CLOSE Close the present notebook * * OTHER module messages * CHIHST Phi-psi plots per residue type (movie) CHSHOW Re-display one step from the CHIHST movie KINFIT Determine dH-activation and T50 from Act vs T curve KINFT2 Determine dH-activation for two loops in 4 curves KINFT3 Determine A and dH-activation from 1 curve KINFT4 As KINFT2 but more restricted in parameter freedom LUIS01 Determine energy parameters for double mutants LUIS02 Determine energy parameters for single mutants ACCEXT Determine accessibility statistics over database ATMATM Calculates atom-atom distance distributions FIND3A Finds groups of 3 amino acids in a similar contact relation GETOBL Reads an O datablock MAKOBL Writes an O datablock MSDB01 Find polymeric units MSDB02 Paste each chain into one molecule MSDB03 List which molecules are "identical" REM290 Make REMARK 290 records for a PDB file REM375 Make REMARK 375 records for a PDB file REM500 Make REMARK 500 records for a PDB file * * PIRPSQ module messages (complete) * DIRPIR Shows list of available pir files SHOPIR Shows one pir file at the terminal GETPIR Adds a pir file to the list SOUPIR Writes (part of) the soup into a pir file DELPIR Removes pir files from WHAT IF'S memory SAVPIR Saves all pir file information in a file RESPIR Restores all pir file information from a file INIPIR Initiates all pir information BLDPIR Model building by homology * * PLOTIT module messages * PLOT Creates a plot file for the FROPLO program PSTPLT Creates a postscript file, and plots it PSTPOS As PSTPLT, but with user defined plot position at paper PSTCPK Creates a postscript CPK file and plots it PARAMS Brings you in the plot parameter menu SAVMAT Saves the present view matrix in a formatted file RESMAT Restores the present view matrix from file SETPST Switches to Postscript plotfile format SETHPG Switches to primitive HPGL plotfile format SETFIG Switches to XFIG 3.1 plotfile format USEMAT Toggles between view from screen and view from file PSVIEW Shows the present view matrix DUBLIT Makes one stero plot from a right and left frame * * PORNO module messages * RIBBON Makes a ribbon, and allows you to add sidechains RIBCPK Makes a ribbon and allows you to add whole residues CARROW Makes a C-alpha trace with N to C terminal arrows HBOFIL Makes a file with hydrogen bonds for RIBBON CACROS Draws crosses at requested alpha carbons PLUTON Activates Ton Spek's PLUTON program APLVIE Apply the present view to the soup WIFRIB Creates a backbone ribbon using David Thomas' software * * QUALTY module messages * RNGQUA does quality control on a residue range NMRQUA does quality control on a series of NMR structures MUTQUA tries all mutants for a range PARAMS brings you in the old style quality control parameter menu QUAPAR show you the old style quality control parameters OLDQUA Calculate first generation quality scores NEWQUA Calculate second generation quality scores*QUAHIDEN QUAFMT Write formatted quality control boxes QUADFT Convert formatted boxes to unformatted FILQUA Show location of quality control boxes * * REFINE module messages * REFI Performs the regularization REFCNT Continues a REFI run (needed if FIX is active) CRUDE Does a very crude first fix of distances REFCYS Crudely closes cys-cys bridges SNAPIT Force atoms to fall on top of other atoms ADDHYD Add protons to residues OPTHYD Optimize proton positions DELHYD Remove protons from a range NOFIX Removes all FIX flags FIXCA Fixes all alpha carbons in a range FIXHAT Fixes all heavy atoms in a range FIXRNG Fixes all atoms in a range ANCHOR Switches the ANCHOR option on NOANCH Switches the ANCHOR option off PARAMS (Re-)sets the regularization parameters * * SHAKE module messages * SHAALL Reconstruct whole soup by shaking SHABLD Model ab-initio using various constraints SHACOL Colour ranges as function of SHAKE violation SHAFIX 'Repair' a loop using SHABLD for just a loop SHAMUL Does multiple SHAALL runs SHARNG Reconstruct part of the soup by shaking * * SCAN3D module messages * PSIPHI Makes phi psi determined group HELSHT Makes secondary structure dependent group SEQUEN Makes sequence determined group ACCVAL Makes group depending on accessibilities CHIVAL Makes group depending on one torsion angle OMEGA Makes group depending on omega DAYHOF Makes group using dayhof homology matrix TURNTP Searches for turns of certain type SCNHYD Makes group depending on hydrophobic moments SCNCYS Searches for (un-)paired cysteines SCNCON Makes group depending on contacts SCNCNS Makes group depending on sequence conservation DGCONT Makes a group of look alike contact pairs DOSCAN Scans protein in soup with Dayhof matrix against database SCNPOS Makes a group as function of position in molecule SCNHBO Makes a group depending on backbone h-bonds NEACON Make a group base on intra-fragment contacs SCNGRA Put group in the movie SCNGRE Put group plus its environment in the movie SCNGRL Put group in MOL-item SCNGRN Put hits middle residue plus neighbours in MOL-item SHOGRP Shows all presently active groups SCNUSE Gets a hit from a group and stores it in the soup SHOHIT Shows hits from a group SANDOR Does logical operations on groups SCNINV Does logical inversion of a group SETLEN (Re-)sets the length of the groups searched for SETEAA Defines so-called self-made amino acids SHOEAA Shows the so-called self-made amino acids PARAMS Go to SCAN3D parameter menu SAVGRP Saves all groups in a file RESGRP Restores all groups from a file INIGRP (Re-)initializes all groups * * SCNSDB messages * SDBACC Shows accessibilities for one database entry SDBHST Shows the DSSP determinations for a database entry SDBCHI Shows all torsion angles for a database entry SDBCYS Shows cys-cys bridges for a sequence entry SDBSEQ Shows the sequence for a database entry SDBPRF Shows sequence preference profile for an entry SDBHBO Shows hydrogen bonded residues for a database entry SDBHMO Shows hydrophobic moment for one entry DINDEX Show database index SHOPAR Show the major parameters for this menu + run DINDEX SEQINF Show sequence information for one entry SHOHED Show the PDB file header for a database entry * * SCAN3D STATS messages * ONEPRF Shows for one position in one group all statistics ALLPRF Shows minimal statistics for all positions in a group ONECHI Shows for one position in one group the chi-1 statistics ALLCHI Shows for all positions in one group the chi-1 statistics GRACHI Puts three dimensional Ramachandran plot in a MOL-item LSTCHI Lists torsion angles for all angles at one position PRFPAI Shows statistics about pairs in one group PARAMS Brings you in the SCAN3D parameter menu * * SELECT module messages * SELINI Initialize all SELECT related parameters SELNMB Search in all PDB files for a certain numerical value SELTXT Search in all PDB files for a certain text string SELSHO Show the columns obtained sofar SELHIT Show the hits in one column SELLST As SELHIT, but with reduced information SELAND Perform a logical AND on two columns SELOR Perform a logical OR on two columns SELINV Inverts one column (TRUE->FALSE and FALSE->TRUE) SELUSE Store hits for usage by the SCAN3D option(s) * * SEARCH module messages * ROWHBO Sets row to TRUE for atoms involved in hydrogen bond ROWACC Sets row according to atom or residue accessibility ROWGAC Sets row according to accessibility of group of atoms ROWPDA Sets all potential H-bond donors/acceptors to TRUE ROWNOH Sets row to TRUE for atoms 'nearby' a water molecule ROW1AA Sets row according to amino acid type ROW1AT Sets row according to atom type ROWNCF Sets row to TRUE for atoms 'nearby' a co-factor ROWSBR Sets row TRUE for atoms/residues involved in a saltbridge ROWSPH Makes a row of atoms within a sphere of an alpha carbon ROWBFT Sets row according to atomic B-factors ROWHST Sets a row according to secondary structure ROWCAV Sets a row for all atoms touching a cavity ROWHSP Sets a row according to HSSP values (mutability) ROWCON Sets a row according to contacts ROWCNR As ROWCON. Puts row constraint on neighbours ROWDIP Sets a row of helix caps ROWMAN Sets a row of residues manually ROWPOL generates a row as function of polarity ROWSHO Shows which rows are active, and their contents ROWHIT Lists a range of amino acids and marks the hits ROWHTO As ROWHIT, but skips residues without hits ROWTAB Writes residues with hits in a table ROWHPR Shows residues plus number of hits per residue ROWHP1 As ROWHPR, but at least 1 hit required ROWINI Resets (=initiates) all rows and their counters etc. GETVAL Reads values from a file, and makes a row GETROW Reads a previously created row MAKROW Creates a file holding the info from one row SAVROW Puts all present rows in a save file RESROW Restores all present rows from a save file ROW1TA Sets all atoms in residue TRUE if one atom is TRUE ROW1T0 Sets all atoms in residue FALSE if one atom is FALSE ROW0TA Sets all atoms in residue TRUE if all atoms are FALSE ROWAND Logical AND on two rows ROWOR Logical OR on two rows ROWXOR (Il-)logical XOR on two rows ROWNOT (Il-)logical NOT on two rows ROWINV Logical NOT on one row (TRUE <--> FALSE) * * SUPPOS module messages * GETMAT Get a matrix from the database PUTMAT Store a matrix in the database LSTMAT Show present matrix plus database DIRMAT Lists entire database contents DELMAT Deletes a matrix from the database GETOLD Reads an external transformation file SHOMAT Shows the presently active transformation RANGE1 Sets range on which to superpose RANGE2 Sets range to be superposed DOSUP Calculates matrix that can place range2 on top of range1 APPLY Applies a matrix to a zone UNDO Undoes the excution of aplly PICKIN Gets superposition sets by picking at the screen APLITM Applies a matrix to a MOL-item SUPOPT Optimizes the present superposition situation SHORNG Shows ranges (after setting superposition ranges) SAVRNG Saves ranges in a file RESRNG Reads ranges from a file INISUP Initializes all parameters relevant for SUPPOS MOTIF Finds the best way to superpose two stretches SFUDGE Average two structures with identical sequences SFUDG2 Average two structures with different sequences ANAFIT Finds the smallest motion to superimpose ranges COMPAR Gives fit statistics EQUAL Compares two covalently identical protein molecules EQUALF As EQUAL, but gets matching residues from a file COLDIF Colour range 2 as function of superposition error CENDIF Calculates residue center distances between ranges CADIFF Calculates Ca-Ca distances between two ranges CABOX As CADIFF, but results are shown as diagonal plot SUPSTS Gives fit statistics ISBEND Find the point of bending in case of domain bending PARAMS Brings you to the suppos parameter setting menu MOTIV This is alternative spelling for MOTIF * * TABLES module messages * TABDIR Gives list of available tables TABDEL Deletes one table TABINI Initializes all table related parameters TABSHO Shows the contents of tables TABGET Reads a table from a formatted file TABLST Writes a table as a formatted file TABOUT Writes a set of tables as a formatted file TABDWN Shifts (part of) a table down TABUP Shifts (part of) a table up TABGRA Puts a table at the graphics window TABPST Plots a table at the laser writer (postscript) TABSAV Saves all table relevant data in a file TABCLU Makes a CLUSTER from a logical table TAB2PR Converts table values into residue properties TABRES Restores all table relevant data from a file TABACC Makes a table of residue accessibilities TABVAC Makes a table out of vacuum accessibilities TABAA Makes a table of residue names TABABF Makes a table of residue averaged B-factors TABBFT Makes an alpha carbon B-factor table TABBMP Make a table of all bumps TABCHI Makes a table with torsion angles TABETM Makes a table with energy values TABEVD Makes a table with integrated electron densities TABHBO Makes hydrogen-bond related tables TABHST Makes a secondary structure table TABNUM Makes a table with simple numerical values TABPIR Makes a table out of a pir file TABPNM Makes table with original pdb numbers TABQUA Makes a table of residue packing quality values TABATV Makes a table out of atomic property values TABPRP Makes a table from residue property values TABADD Adds two tables TABSUB Subtracts two tables TABMUL Multiplies two tables TABMIN Determines the pairwise minimum of two tables TABMAX Determines the pairwise maximum of two tables TABAVE Determines the pairwise average of two tables TABAVM Determines the average of more than two tables TABCOR Determines correlation between tables (after shifting) TABMOD Executes modulo operation on a table TABSQ2 Squares a table TABAAC Make table of residue type PDB average accessibilities TABSMC Number of symmetry related contacted residues TABCAA Generate residue type statistics for a table TABADF Determine angular distance between angle tables TABDIF Put a character mark if two tables differ 'too much' TABDF2 Put a numerical mark if two tables differ 'too much' TABCUP Toggles continuous updating of tables at graphics screen TABSCT Make a scatter plot for two tables TBLVGT Create a logical table as for numerical table > cutoff TBLVEQ Create a logical table as for numerical table = cutoff TBLINV Inverts a logical table (TRUE <--> FALSE) TBLAND Makes table of logical AND on two tables TBLOR Makes table of logical OR on two tables TBLSTS Counts TRUEs and FALSEs per residue type TBLDFC Makes logical table of comparison of character tables * * WATER messages * SHOWAT Lists groups of water molecules and number of H2Os LSTWAT Lists a range of water molecules WATNAA Lists all waters near a residue NAAWAT Lists the nearest residue for every water NALWAT Lists all near residues for every water DBLWAT Lists all waters that contact two ranges STSWAT Gives statistics on water positions CABWAT Determines Ca-Cb orientation relative to nearest bulk water POTWAT Predicts waters around a residue MOVWAT Applies all matrices to bring h2o's near a range NETWAT Draws a net over a group of water molecules COPWAT Allows you to make sub groups of waters by hand DUPWAT Make multiple copies of touching symmetry related waters CHKWAT Same option as H2OCHK in CHECK menu SPLWAT Splits water in eigth groups PARAMS Brings you to the water parameter menu * * WALCOR related messages * CORMUT General basic correlated mutation finder CORMUM As CORMUT, but using a scorings matrix CORMUN As CORMUT, but without the variability contribution CORMUF As CORMUT but with a different scorings scheme CORAN1 Searches for correlations against a CMC file CORAN2 As CORAN1 but with a different scoring scheme CORPM1 As CORAN1 but with a different scoring scheme CORPM2 As CORAN1 but with a different scoring scheme CORGR1 As CORAN1 but with a different scoring scheme GETCMC Sort the BIGFILE according to the sequence order in CMC file GETTIT As GETCMC, but also reads new titles from the CMC file MAKCMC Write a CMC file that corresponds to the BIGFILE SRTCMC Sort a CMC file according to the CMC code MAKTFF Creates a skip file for conserved residues MAKPTF Creates a skip file for conserved residues, using CMC input * * WALGRA related messages * GRASQS Display sequences graphically COLSQS Allows for the modification of the residue colour list SHOW Used in the WALIGN related menus, makes GRASQS interactive 2DPLOT Displays sequence as 7-tubes through membrane plot (for GPCRs) PRETYG Pretty drawer for multiple sequence alignments PRETYP As PRETYG, but now for postscript output * * WALIGN messages * WALCOR Activates the mutation correlation menu WALGRA Activates the graphical sequence menu WALPRF Activates the sequence profile and alignment menu WALSEQ Activates the sequence administration menu WALSRT Activates the sequence sorting and selection menu WALINI Initializes all alignment parameters BIGFIL Opens a (new) big file for sequences/profiles ORGBCK Overwrite aligned sequence(s) with original (unaligned) copy BIGSTS Counts number of profiles and sequences in BIGFILE SETMAT Sets/reads a alignment scorings matrix SHODAY Displays present scorings matrix at terminal 2ALIGN Align 2 sequences MAKHSP Write sequences in HSSP format file SHOIDM Shows pairwise sequence identity matrices HISTID Make histogram of identity percentages between sequences MFETCH Makes a list of file namess that can be used by GCG's FETCH MFILES Makes the file FILES.LIST, needed for the server PARAMS Brings you in the alignment parameter menu WLHPID Graphical display of pairwise similarities WLHLFK Read sequences from LFK style file WLHGAP Over-rule profile gap penalties with those from PARAMS WLHLFD Reads sequences from LFK-daily-update-files WLHFIN Checks if the Brh aligned sequences have the GPCR fingerprint WLHDFN Delete sequences that do not have the GPCR fingerprint WLH1ST Does the whole 7TM HSSP process for one molecule class WLHSWS Reads sequence(s) from set of combined swissprot files WLHDNA Delete DNA sequences from the BIGFILE WLHL2S Read sequences from a 'list2seq' file (alternative FASTA) WLHDFR Delete fragments from the BIGFILE WLHCLU Cluster sequences after alignment WLHSPA List WALIGN related common parameters and values WLHCPL Creates the file PDB.LIS WLHPCR Searches for decamers that can be good PCR probes WLHWIN Writes unaligned sequences as single records in a file WLH2ST As HIDE08, but including gap penaltie updates WLHRIN Reads sequences back that were written with HIDE17 WLHGWT Searches in sequences for a fragment of requested weight WLHWIA Writes aligned sequences as single records in a file WLHXXX Does somthing too.... WLHSPR Runs all sequences against all profiles WLHNAP Converts DNA sequence into protein sequence PHYTRE Draws phylogenetic tree EMBED3 Embed sequence space in 3 dimensions PLOT2D Alternative spelling for PLOT2D * * WALPRF messages * GETPRF Reads a profile from a file DELPRF Deletes a profile from the BIGFILE DELPRS Deletes multiple profiles from the BIGFILE (slow option) MAKPRF Writes a profile in a profile-file DIRPRF gives a list of the profiles presently in the BIGFILE LSTPRF Lists the sequence information of a profile SHOPRF Lists all information of a profile ALIPRF Aligns sequences against a profile PRFSWT Update sequence and residue weights UPDPRF Updates a profile after alignment UPAPRF Updates a profile after alignment, including gap penalties NEWPRF Makes a new profile from (aligned) sequence(s) CNVPRF Convolute profile with scorings matrix SOUPRF Makes a profile for all protein in the SOUP AL2PRF Aligns two profiles PCTPRF Determines convolution between sequences and a profile INSPRF Puts an insertion in a profile SEQPRF Writes one sequence out as a profile file MAKMSF Write multiple sequence alignment as a MSF GETARB Reads arbitrary sequence numbers from a profile * * WALSEQ messages * GETSEQ Reads sequence(s) from file DIRSEQ Gives directory of sequences/profiles in big file LSTSEQ Lists complete info about sequence(s) LSTSQS List residue(s) for range of sequences DELSEQ Deletes sequence(s) from the big file MAKSEQ Write out sequence in sequence file CCNSEQ Concatenates two sequences MAKINT Write sequence(s) in WHAT IF's formatted format GETINT Read sequences back from a WHAT IF format formatted file * * WALSRT messages * DELNAM Delete sequences with certain text in title DMATCH Look for nearly identical sequences DOUBLS Look for identical sequences KPNAME Only keep sequences with certain text in title KWCHEK Allow logical expressions for DELNAM or KPNAME KILDBL Remove sequences that occur for a second time UNKTYP Determines for unknown sequences the class DELALI Deletes sequences with insufficient overlap with a profile SRTPCT Sorts sequences as function of overlap with a profile SRTPID Sorts sequences as function of identity with a profile SRTACC Sorts sequences by numerical part of accession code SRTGMB Sorts sequences as function of grey meatball character SRTFLN Sorts sequences by file name * * WALSRV messages * GPCINI Initialize the big server file GPCOPE Open the existing big server file GPCSTS Show all statistics about the big server file GPCSRC Shows only the summary statistics about the big server file GPCGCL Read the classes from _7TM.CLASSES GPCGPR Get the profile information from _7TMPROF.LIST GPCRPR Read the profiles obtained with GPCGPR GPCSPL Uses the profiles to classify the sequences and sort them GPCSEL Uses the profiles to classify the sequences. Dont sort them GPCMAL Loop over all classes and make HSSP, MSF, etc. GPCO7T Read the 7TM directories file GPCG7T Gets the files from 7tmrlist.txt local * * XRAY related messages * EVADEN Convolutes bell shaped atoms with the density map EVACAS As EVADEN, but for alpha carbons only RSRSID Optimizes side chain density fit by torsion rotation RSRRES Rigid body translational density fitting, whole res RSRBB Rigid body translational density fitting, backbone PEPFLP Flips one peptide plane. RNGFLP Inverts backbone direction. MASMAP Go to the map massage menu (mainly for X-ray) MAPEDT Go to the enveloppe map editor menu * * DSSP messages * SHOHST Shows the secondary structure of a protein SHOSSS As SHOHST, but adds accessibility and symmetry contact info INIHST Forces WHAT IF to redetermine the secondary structure EDTHST Allows for manual modification of secondary structure ALLHEL Forces WHAT IF to thing that all residues are helical ALLCOI Forces WHAT IF to think that all residues are coil SUMHST Determine secondary structure percentages in the soup WIFHST Forces WHAT IF to use its internal emulator and not DSSP CHKHST Determines the correlation between DSSP and its emulator HSTMTS One day this option will improve sec. struc. determinations . ORGDSP Replaces converted HST in database by original DSSP values GETDSP Reads the C-alpha coordinates from a DSSP file ALCOIL Alternative spelling for ALLCOI NEWHST Alternative spelling for INIHST * * Symmetry messages * SOUSHL Add all residues in a shell to the soup SOUBOX Add all residues in a box to the soup SOUSPH Add all residues in a sphere to the soup SOUSRS Add all residues in a sphere around a residue SOUCEL Add all molecules in the unit cell to the soup SOUSM1 Apply one symmetry transformation to the soup. SOUSYM Apply all symmetry transformations to the soup. GRASHL Show all residues in a shell in a MOL-item GRABOX Show all residues in a box in a MOL-item GRASPH Show all residues in a sphere in a MOL-item GRASRS Show all residues in a sphere around a residue GRACEL Show all molecules in the unit cell GRASM1 Show one symmetry transformed molecule GRASYM Show all symmetry transformed molecules CELCKM Check many CRYST1 and SCALE cards. CELSHO Show CELL, and SCALE and INVERSE SCALE transforms CELINP Input cell parameters via the keyboard CELNEW Check whether the conventional cell makes symmetry CELAPP Apply the transformation to the conventional cell LCKSYM Toggle locking of symmetry matrices USESYM Toggle usage of symmetry in other options SYMDEL Delete individual transformations SYMINI Clear all transformations SYMSAV Put transformations to file SYMRES Get transformations from file SYMSHO Show all transformations SYMINP Input transformations via the keyboard SYMSPG Add the transforms implied by Spacegroup Symmetry SYMIIT Input transformations in Int. Tables format SYMRDU Remove duplicate transformations SYMPNI Print message for non-integral rotations SYMPAR Set parameters for the symmetry routines SYMDSM Delete symmetric molecules from the soup SYMGCA Toggle CA-only flag for GRA options in SYMTRY menu SYMISG Input the space group via the keyboard SYMNEA Find transforms. that create "NEAR" molecules SYMCGP Check if transformations form a closed group. SYMDNT Delete syms that do not produce touching mols. SYMPIC Translate transformations to the unit cell. SYMANA Analyze bad inter-symmetric contacts. SYMAMB Disambiguate cells unsing bump analysis SYMMOV Move a residue into close contact * * VDW module messages * VDWATT (Re-)sets the VdW radii according to atom type VDWBB (Re-)sets VdW radii for the backbone without =O VDWBBO (Re-)sets VdW radii for the backbone =O VDWSS (Re-)sets VdW radii for the side chains VDWCA (Re-)sets VdW radii for the alpha carbons VDWRNG (Re-)sets VdW radii for a range of residues * * PARAMS module messages * LINCOL Colour of lines made with screen option .LINE LINMOD Line type for the lines made with screen option .LINE AA1OR3 Amino acid output in 1 or 3 letter code flag INSFLG Amount of sequence output flag in SCNSDB menu VDWOVR Bump/contact distance between Van der Waals radii DFBFAC Default B-factor CYSCYS Do/don't use inter chain cys-cys bridges NEICON Use covalent neighbours in BUMP/CONTAC like options * * PARDG module messages * DGCERR Maximal Ca-Ca distance misfit allowed DGTERR RMS Ca misplacement allowed DGSHWT Maximal number of hits to be shown by DGSHOW ADDFIT Additional backbone fit flag MXCAER Maximal Ca misplacement after real suppos INANCH Number of anchoring residues at each side in DGINS USEACC Should accessibility constraints be used? LOWACC Lower limit on accessibility of database hit HGHACC Upper limit on accessibility of database hit CNTERR Maximal error in DGCONT option * * PARCON module messages * CONLIN Draw lines to indicate bumps or contacts FRMCOL Colour of frame around plot SEQCOL Colour of sequence characters in frame NEICOL Colour of neighbouring residues after picking CACFLG Flag for making Ca-crosses or not 1O3FLG Flag for one or three letter code residues HOFFLG Flag to skip lower triangle CACCOL Colour of ca-crosses in squares BOXTYP Type of boxes in graphics SHOPAR Show parameter values * * PARQUA module messages * LEVOUT Level of output in Quality Control SKPNEI Skip main chain of neighbours or not flag WEIGHT Flag for type of neighbour weighing WAYQUA How to give values, nearest point or convolute * * PARSCN module messages * HITBBF What to show of the hit itself? HITNAF What to show of the hits environment? SCONTP SCNCON on one residue or whole stretch? HITOUT Flag to determine where SCNGRN hits should go * * PARGRO module messages * MINTYP Energy minimization method STEPS Number of energy minimization steps NEWGRD Steps per new gradient ISHAKE Flag for using SHAKE or not MINDIF Minimal allowed energy difference between steps STPSIZ Step size in steepest descent minimization MAXSTP Maximal step size in steepest descent minimization RCUTP Cutoff radius for the pair list generation RCUTL Cutoff radius for long range coulomb interaction TEMP Temperature during md run TEMPER Maximal deviation of temp in MD run MDSTEP Number of picoseconds in an MD run HTSTEP Number of heatup steps in an MD run FIXCAS Fix alpha carbons flag FIXFRC Force with which to fix alpha carbons LEVUSE Determines level of interaction TRAJEC Flag for writing trajectories or not TRASTP Number of MD steps per written trajectory HPLACE Determines how hydrogen positions are generated MDINIT Determines how the MD run is initialised. XTCASC Determines how trajectories are written * * PARBLD module messages * BLDTYP Flag for guided or default building HELIX Build with helical guide angles (-57,-57,180) SHEET Build with strand guide angles (-150,150,180) BLDPHI Phi in case of guided building BLDPSI Psi in case of guided building BLDOME Omega in case of guided building * * PARWAT module messages * NAYWAT Flag for .NAYB action in case waters are involved NEWGRP Flag for making new water groups or not NETDST Water-water distance cutoff in NETWAT option VDWDST VdW-VdW distance cutoff in other WATER options * * PARPLT module messages * LINTYP User defined or colour dependend line types * * PARHBO module messages * DONACD Maximal donor acceptor distance HYDACD Maximal hydrogen acceptor distance ANGERH Maximal error in donor - hydrogen - acceptor angle ANGERA Maximal error in hydrogen - acceptor - X angle HBOTYP Mode for drawing hydrogen bonds * * HYDMOM module messages * WINDOW Width of the window PROPTY Property type number ANGLEM Repeat angle for moment calculation * * PARNEU module messages * TEMPNW Initial 'temperature' of the training TEMPNE Maximal allowed deviation in TEMP LINEAR Toggles the linear mode of the net ON/OFF ROBUST Toggles between quadratic and robust errors SMTERR Toggles between quadratic and cubic errors. * * PARTRA module messages * PCWHAT Determines what can all be picked in a trajectory * * PARACC module messages * ACPREC Precision for accessibility calculations ACCTYP Type of accessibility calculation LIMBUR Limit for a residue for being called buried USESLF Do or do not add 'own' molecule to environment WATRAD Radius of the water probe OUTACC Flag for output of accessibilities in PDB file * * PARSUP module messages * MINLEN Minimal number of residues needed in a stretch in MOTIF option MAXERR Maximal pairwise alpha carbon misfit allowed RMSERR RMS pairwise alpha carbon misfit allowed NONHEL Required number of non-helical residues in fragments LENHOM Number of consecutive residues used in SUPOPT * * PARREF module messages * NCYCS Number of cycles NITS Number of iterations per cycle ZSCO Desired maximal Z score on any parameter REFLEV Sophistication level of REFI FIXREF Force by which FIXed atoms are pulled back WRNLEV Sigma cutoff above which WHAT IF starts mumbling USEBAD Repair also bad atoms or patch up good ones only * * PARGRE module messages * ARRFAC Scale factor for arrows ARRLIN Number of sides of an arrow ARRCOL Colour of arrow ARRLNP Length of arrow point ARRLNS Length of arrow base ARRTHP Thickness of arrow point ARRTHS Thisckness of arrow base RADIUS Radius of PLUTO atomic spheres STICK Radius of the PLUTO sticks representing bonds LINES Number of lines making up the PLUTO bond sticks * * PARGRI module messages * ALHY Hydrogen bonded hydrogen polariaability EFHY Number of electrons per hydrogen bonded hydrogen IHVA Energy parameter mode for hydrogen bonded hydrogen QQHY Charge of hydrogen bonded hydrogen VDHY Hydrogen Van der Waals radius SHOPAR List the values of the parameters CLER Clearance in angstroms around the target DPRO Dielectric constant of macromolecule DWAT Dielectric constant of solvent (water) EMAX Energy value inside macro molecule FARH Distance cutoff for hydrogen bonds FARR Distance cutoff for lennard jone interactions KWIK Turbo boost flag LENG Length of output tables LEVL Amount of output flag LIST Needed in case of multiple runs for one grid NETA Number of extra target atoms NPLA Number of grid planes per angstrom NUMB Number of minima listed per section SECLOW Lowest section to be calculated SECHGH Highest section to be calculated * * PARWAL module messages * GAPOPE Gap open penalty for sequences GAPELO Gap elongation penalty for sequences PRFOPE Gap open penalty for profiles PRFELO Gap elongation penalty for profiles SEQSCO Minimal sequence identity score in GENPRF PRFSCO Minimal profile convolution in GENPRF CHRSIZ Character size for PRETY* options LIMBOX Number od identities needed for boxing in PRETY* RESLIN Number of residues per line in PRETYP * * PARCOL module messages * LOWCOL Lower colour of a colour range (1-360) HGHCOL Higher colour of a colour range (1-360) * * PARCNL module messages * ANGLEC Courseness of the triangulation of the surface CONRAD Radius of the probe used to define the surface
0 blue
60 purple
120 red
150 orange
180 yellow
240 green
360 blue
When you choose numbers inbetween, you will get colours inbetween.
These colours are all fully saturated, if you want to mix in some white,
you should use the SATURA parameter (see chapter on parameter settings).
WHAT IF> GENERATED 3SSP FILE
## 136 ## 1GOX ! Name of the database file used as master molecule
1 2 3 4 5 6 !sequence #
MEITNVNEYEAIAKQKLPKMVYDYYASGAEDQWTLAENRNAFSRILFRPRILIDVTNIDM !sequence
TTTHHHHHHHHHT HHHHHHHH TTT HHHHHHHH3333SSS T T S !DSSP
1 2 3 4 5 6
TIMTLSSWATSSVEEVASTGPGIRFFQLYVYKDRNVVAQLVRRAERAGFKAIALTVDTPR
SSS TT TT HHHHHTT SSSSS STTHHHHHHHHHHHHHTT SSSSS T TT
1 2 3 4 5 6
SLSWKDVAWLQTITSLPILVKGVITAEDARLAVQHGAAGIIVSNHGARQLDYVPATIMAL
T HHHHHHHHHH T SSSS THHHHHHHHHTT TSSSS 333TTTTT HHHHH
1 2 3 4 5 6
PVVFSLAAEGEAGVKKVLQMMRDEFELTMALSGCRSLKEISRSHIAADWD
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT TSTTT 333SSSTT
## 1 156B AA= 100 ! name of the first database file tested
++++ MAXIMAL NUMBER OF SINGLE HITS: 52
! AA=100 means that 156B has 100 amino acids.
! the line ++++ MAXIM... etc. means that if only single alpha
! carbons are looked at, 52 can be superposed simultanuously.
! this of course is scientifically insignificant. However if
! this number reaches 90 percent of the full length, you might
! want to inspect this alignment by hand because WHAT IF might
! have missed the answer.
## 2 1ABP AA= 306
++++ MAXIMAL NUMBER OF SINGLE HITS: 123
## 3 1CC5 AA= 83
++++ MAXIMAL NUMBER OF SINGLE HITS: 54
## 4 1CRN AA= 46
++++ MAXIMAL NUMBER OF SINGLE HITS: 46
## 5 1CTF AA= 68
++++ MAXIMAL NUMBER OF SINGLE HITS: 57
## 6 1FX1 AA= 147
++++ MAXIMAL NUMBER OF SINGLE HITS: 103
1 2 3 4 5 6
PKALIVYGSTTGNTEYTAETIARQLANAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWG
SSSSS S TTTHHHHHHHHHHHHHHTTT SSSSS TTT TTTTTT TSSSS S SS
1 2 3 4 5 6
CGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAI
THHHHHHHHHHHTTT SS T SSSST 3333HHHHHHHHHHHHHH
! The fact that a sequence is shown means that WHAT IF has
! has found a 3-D alignment
##L 88 GLY (88 ) <-> 41 GLU (42 ) TILL 92 THR (92 ) <-> 45 LEU (46 )
! This line indicates that residues 88-92in the master molecule
! fall on top of 42-46 in 1FX1. The numbers between brackets
! give the name of the residue in the PDB file.
GEYAT ! sequence in master structure
HHHHH ! DSSP for sequence in master structure
EAGGL ! sequence of matched fragment in database hit
TTT ! DSSP for matched fragment in database hit
##L 108 TRP (108 ) <-> 70 PHE (71 ) TILL 112 SER (112 ) <-> 74 PHE (75 )
WATSS
T TT
FIPLF
THHHH
##L 138 ALA (138 ) <-> 105 ASP (106 ) TILL 154 LEU (154 ) <-> 90 PHE (91 )
AQLVRRAERAGFKAIAL
HHHHHHHHHTT SSSS
DAIEEKLKNLGAKVACF
HHHHHHHHTTT SSSSS
##L 293 ALA (302 ) <-> 29 GLY (30 ) TILL 299 GLY (308 ) <-> 35 ARG (36 )
AAGVFIG
TSSSS
GYEVDSR
T SSSSS
.....
.....
.....
## 23 1UBQ AA= 76
++++ MAXIMAL NUMBER OF SINGLE HITS: 51
## 24 ESEC AA= 274
++++ MAXIMAL NUMBER OF SINGLE HITS: 197
SOUADM(ISOUP,1) pointer to first residue in molecule
SOUADM(ISOUP,2) pointer to last residue in molecule
SOUADM(ISOUP,3) number of residues in the molecule
SOUADM(ISOUP,4) number of atoms in the residue
SOUADM(ISOUP,5) molecule type:
1) protein
2) multi atomic drug or ligand or co-factor (simply
called drug throughout this writeup)
3) DNA or RNA
4) single atomic drug ligand or co-factor
SOUADM(ISOUP,6) pointer to first connectivity in drug connectivity
table
SOUADM(ISOUP,7) pointer to last connectivity in drug connectivity
table. These two pointers are only set if
souadm(isoup,5)=2
SOUADM(,) is an integer array.
The soup is organized such that proteins and nucleic acids come first, thereafter come the drugs, and finally the water molecules. This of course is not needed as you will see when you read this appendix carefuly, but it makes it easier to add subroutines to the program on the long run this way.
At the entity level several arrays are being used. For entity IAA the following information is kept in common:
PNTAAS(IAA) pointer to first atom in IAA. (INTEGER).
PNTAAC(IAA) pointer to alpha carbon in IAA (if IAA is an amino
acid). (INTEGER).
PNTAAE(IAA) pointer to last atom in IAA. (INTEGER).
CHAINN(,IAA) CHAINN(1,IAA)=1 for the N-terminal residue in a chain,
The C-terminal residue becomes 3. All other residues get
the value 2. CHAINN(2,IAA) contains the number of the
molecule of which this residue is a part.
ONESA3(IAA) type indicator of the entity. For amino acids this is
ALA, CYS, etc. For nucleic acids DCYT, DGUA, etc is
used. No rules for nomenclature exist for drugs. Waters
are called H2O. (CHARACTER*4).
ONESA1(IAA) holds the character*1 representation of ONESA3(). I
don't think this array is ever used yet in WHAT IF.
(CHARACTER*4).
NUMNAM(IAA) This is the user given name to the entity. No rules
exist, but it is best to keep all NUMNAM()'s in the soup
unique. Mostly NUMNAM()'s are just sequential numbers.
(CHARACTER*4).
ACCDON(IAA) flag that becomes true if the accessibility for this
entity has been calculated. (LOGICAL).
AAISOK(IAA) flag that becomes true if the checks for nomenclature
and completeness are all ok for a residue. (LOGICAL).
SPHRAD(,IAA) information about the smallest sphere that can hold the
entity. The first three numbers are the x-, y-, and z-
coordinate of the center, and the fourth coordinate is
the radius. (REAL).
SUMACC(IAA) holds the sum of the accessibilities of all atoms in the
entity. (REAL).
PRPVAL(IAA) The property moments (see the appendix on hydrophobic or
property moments) are stored in this array. (REAL).
XYZCAS(,IAA) This array is often used to temporarily store the x-,
y- and z-coordinates of the alpha carbons of amino acids
in case they need to be changed for a short time (REAL).
CHIANG(,IAA) holds phi, psi, omega, and chi-1 till chi-5 for amino
acids. (REAL).
ETMTOT(,IAA) holds for every energy term the sum of all individual
atomic contributions. (REAL).
AMODEL(IAA) flag that is true if IAA is activated for the working
model. (LOGICAL).
LOCHST(IAA) secundary structure determination by DSSP (CHARACTER*1).
XCOORD(IAT) x-coordinate of atom IAT. (REAL). YCOORD(IAT) y-coordinate of atom IAT. (REAL). ZCOORD(IAT) z-coordinate of atom IAT. (REAL). XBFACT(IAT) crystallographic b-factor. (REAL). ACCESS(IAT) atomic accessibility for water. (REAL). WEIGHT(IAT) occupancy. (REAL). VDWRAD(IAT) Van derWaals radius. (REAL). ONESAT(IAT) name of the atom, eg. CA, N, P, CD1, etc. (CHARACTER*4). ATCOLR(IAT) colour of IAT (0-360). (INTEGER).
NUMAAT total number of entities. NUMAAF total number of residues. NUMATF total number of atoms. NUMCOF total number of drugs. NUMCON total number of drug connectivities. NUMSOU total number of molecules (excluding waters) in the soup
DO 30 ISOUP=1,NUMSOU
DO 20 IAA=SOUADM(1,ISOUP),SOUADM(2,ISOUP)
DO 10 IAT=PNTAAS(IAA),PNTAAE(IAA)
here you can do something with the atom
10 CONTINUE
20 CONTINUE
30 CONTINUE
IF (NUMH2O.GT.0) THEN
DO 40 IH2O=PNTAAE(NUMAAT)+1,NUMATF
here you can do something with a water molecule
40 CONTINUE
END IF