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* * 3SSP module messages * MAK3SP Creates a 3ssp file SUM3SP Makes a summary of a 3ssp file FILTER Removes bad hits from 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 * E: 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 TABACC 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 GRAACC Puts accessible dot surface at the graphics GRAVDD Puts Van der Waals dot surface at the graphics * * TRAMOV module messages * E: 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) USEALL Mark all atoms 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 BNDCHK Makes sure that bonds over boundary are not displayed PROJEC (Re-)sets the project number PARAMS Brings you in the ANATRA parameter menu * * ANATRA module messages * E: ANAHBO Analyse a hydrogen bond during the trajectory ANAVOL Determine the volume ocupied by an atom 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 PROJEC (Re-)sets the project number 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. WADSSP Use DSSP instead of TRAGEO routines for calculations. 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 * E: 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 * E: 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 BMPCHK Looks for too short interatomic distances BNDCHK Checks bond distances BPOCHK Search for buried unsatisfied H-bond donors/acceptors 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 MVMCHK Matthews coefficient (Vm) and other cell volume checks NAMCHK Does a nomenclature check NEWCHK Throw away the old summary file PLNCHK Check protein side chain planarity PL2CHK Check atoms connected to aromatic rings for planarity PUCCHK Verifies ring puckering in Proline residues QUACHK Does packing quality control 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 * E: 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 * * FAMCLU module messages * E: INICLU Initializes all clusters INIFAM Initializes all families HYDCLU Creates a cluster of buried hydrophobic residues SETCLU Manually defines a cluster of residues SETFAM Creates a family SHOCLU Lists all clusters SHOFAM Lists all families * * COLOUR module messages * E: 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 COLCHG Colour by atomic charge 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 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 * E: 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 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 BUMPS Lists all atomic bumps * * CELL module messages * E: SHOCEL shows all coordinate and map cell dimensions. D: SHOCEL toont alle cel dimensies zoals uit koordinanaten of maps gelezen * * DGLOOP module messages * E: 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 DGCONT Finds pairs of residues with similar contacts SHOGRP 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 INIGRP Re-initiates all groups SETLEN Re-sets the length of the groups DGR1-1 Finds rotamers for one type at one position (=DGROTA) 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 GRPSTS Activates the statistics-on-groups menu (=SCNSTS) * * 2D-3D module messages * E: 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 DIGPCK Pick the corner points DIGSAV Save digitized points in a file DIGRES Restore digitized points from a file DIGOPT Optimise 3D coordinates with 2D and 3D restraints DIG2T3 Reconstruct 3D from 2D coordinates DIGSH2 Show current 2D coordinates in the XFIG coordinate system DIGTGT Tighten 3D restraints on Ca-Ca distances DIGREL Relax 3D restraints on Ca-Ca distances DIGSHO Show digit parameters * * DOSELF module messages * E: DOCUWI Put text for placeholders in a WHAT IF source module PRETTY Prints a WHAT IF source module nicely readable COUNTR Counts source code statistics over WHAT IF modules RUNOFF Emulates RUNOFF for one chapter of the writeup RUNALL As RUNOFF but for many chapters TEXALL As for RUNALL, but produces also TEX output CHKMES Translates/corrects Dutch lines in MESSAGES.TXT * * DRUG module messages * E: 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 FLEXX Dock a flexible small molecule using FLEXX 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 INIDDB DOCKDB gets started (should be done first, but only once) * * ESSDYN module messages * E: WEDALL \ WEDTRA \ WEDEIG \ WEDPRJ \ ANWTRA \ ANWEIG |-> Here Dumb Daantje and Buggy Bertje will type something ANWPRJ / PRNSEL / WEDSEL / SELMAS / SELFIT / * * EXTRA module messages * E: 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 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 MAKPRF Attempts to make threading profile * * GRAFIC module messages * E: 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 inetractive 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. * * GRATWO module messages * E: PHIPSI Makes phi-psi 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 LABATM Writes text next to atom PARAMS Activates parameter modification menu * * GRAEXT module messages * E: 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 between 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 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 * * GRID module messages * E: 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 SAVMAP Saves all present map parameters in a file RESMAP Restores all present map parameters from a file SETBOX Resets the limits of the GRID map SHOMAP Shows all maps presently in memory GETGRD Reads in a GRID result map PROJEC Sets the project number PARAMS Sets parameters for GRIN/GRID * * GROMOS module messages * E: 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 CHGCYS Change the status of inter molecular cys bridges 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 GCHECK Checks the soup for typical GROMOS nomenclature errors TRSFIL Creates torsion angle constraint cards for EM/MD job WMERGE Merges two topology files SHOGMT Shows results of last PROGMT run SHOGCH Shows results of last PROGCH run SHOMMT Shows results of last PROMMT run SHOEM Shows results of last PROEM run SHOMD Shows results of last PROMD run SHOBOX Shows results of last PROBOX run * * HBONDS module messages * E: SHOHBO Give hydrogen bonds between two ranges SLFHBO Looks for intra residue hydrogen bonds only GRAHYD Puts hydrogens in a MOL-item HBOSTS Does statistics on hydrogen bonds 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 HB2XST Extra statistics about the hydrogen bonds * * HYDRO module messages * E: 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 * E: 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 * E: ITEMON Switches a MOL-item on ITEMOF Switches a MOL-item off OBJON Switches a MOL-object on OBJOFF Switches a MOL-object off DELITM Deletes a MOL-item INIOBJ 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 INIGRA 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 NOMODL Deletes the working model * * LABEL module messages * E: 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 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 * * MAKDB module messages * E: PRP001 Corrects all PDB files 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 Creates nearest neighbour type distance tables PRP015 Puts the eigth torsion angles as term 10 in alcoor PRP016 Makes the secondary structure element tables PRP017 Makes the nearest neighbours index tables 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 PRP022 Reserved for future use PRP023 Reserved for future use PRP024 Reserved for future use PRP025 Reserved for future use PRP026 Reserved for future use PRP027 Reserved for future use PRP028 Reserved for future use GETORG Overwrites the HST values in common with originals MAKFMT Creates a formatted coordinate file (ALCOOR.XYZ) GETFMT Regenerates database coordinates from formatted file (ALCOOR.XYZ) PRPCHK Checkes if all PDB files required for database generation exist HIDE01 Copy all PDB files to default directory HIDE02 regenerate PDB.LIST from the database HIDE03 checks if all HSSP files exist HIDE05 creates formatted ALCOOR.FMT HIDE06 recreates ALCOOR.XYZ HIDE07 creates formatted HSSP derived files HIDE08 re-creates real HSSP derived files HIDE09 Creates all atom verification force field HIDE10 Creates the 1-3 bond table for amino acids HIDE11 Creates BUMPS.PCT (allowed shortest distances) * * MAP messages * E: GETMAP Reads an map into WHATIF GETFMP Reads a formatted map MAKFMP Writes a formatted map GETXPF Reads a formatted XPLOR map PARMAP Change map-related parameters DEFMAP Changes the default map MAKMAP Writes the present default map to disk (not needed) DELMAP Removes a map from WHATIF`S memory INIMAP Removes all maps from WHATIF`S memory SRFMAP Creates an accessible surface contour map CAVITY Creates an electron density map for cavities AACAVI Shows residues that touch cavities SMLCAV Calculates local cavity more precise CONMAP Calculates map that represent contacts between subunits PRBRAD (Re-)set the probe radius for cavity calculations GRAMAP Sends contours to the graphics window GRACOL As GRAFST, but with coloured lines GRAXYZ As GRAMAP, but contours only in one direction 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 DENMAP Shows density at terminal screen (debug option) AXMAP Puts axes along the shown map fragment CHKMAP Checks a map * * MAPCON module messages * E: MAKCON Creates files needed to run Connolly`s program RUNCON Runs Connolly`s program LSTCON Get PQMS or TRB related files in the editor PROJEC (Re-)sets the project number 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 * E: GETENV Reads an envelop into the main map GETMAP Reads a map into the main map PARMAP Change map-related parameters DEFMAP Changes the default map DENMAP Show map density values in the text window SHOMAP Inspection of map-related parameters and grid values GRAMPP Activates the interactive editing option FIX0 Switch from toggle picking to fixed 0 setting FIX1 Switch from toggle picking to fixed 1 setting NOFIX Switch (back) to toggling upon picking * * MASMAP related messages * E: 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 * E: GETMDF Reads an MDF LSTMDF Lists reflections at the terminal WILSON Creates a Wilson plot for one column COLUMN Lists the column numbers DIFSTS Give statistics on the difference of two columns SETBIN Sets bin boundaries for COLBIN GRAMDF Puts the requested dots at the screen TRGALL Switches all reflections on TRGSIZ Switches refs on as function of size TRGDIF Switches refs on as function of difference TRGABS Switches refs on as function of absency TRGRES Trigger as function of resolution TRGHKL Trigger blocks of H K L REMNBT Switches refs off if not in two columns COLALL Give all refs one colour COLSIZ Colour refs as function of their size COLDIF Colour as function of two columns difference COLBIN Colour per size bin COLABS Colour as function of absent/present * * MOL module messages * E: 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. 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. HIDDEN Display hidden options E: 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 FIXDNA Runs a couple corrections on DNA with bad nomenclature SHOTOP Shows the contents of the presently used topology file * * NEURAL module messages (complete) * E: 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 SMOOTH Uses different weigths to distribute errors more evenly SHOSET Shows data set with measured and predicted output NETWRK Allows you to define the network architecture GRANEU Does not work yet GETNEU Reads neuron (junction) values from a file TRAIN Executes training run(s) for the network 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 SHAKE 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) * E: USEMLS (Re-)define the molecules to be used SUPMLS Superpose all molecules to be used CHKMLS Checks if a the molecules are covalently identical GETDIA reads coordinates from a DIANA file GETUXM Read Bruker UXNMR 3D-NMR map MOTMLS Does a MOTIV 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 SHOMLS Display all atoms of all molecules to be used BBBALL Display backbone in (small-)ball and stick mode GRABBD As BBBALL, but without H`s atoms NOESIM Runs Bob Bywaters NOESIM NOE-simulation program 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) * E: 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 INDEX Show the index of the general notebook CLOSE Close the present notebook * * OTHER module messages * E: 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 GETOBL Reads an O datablock MAKOBL Writes an O datablock * * PIRPSQ module messages (complete) * E: 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 * E: 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 USEMAT Toggles between view from screen and view from file PSVIEW Shows the present view matrix * * PORNO module messages * E: 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 SPLINE Creates a backbone ribbon using David Thomas' software * * QUALTY module messages (Not all options exist anymore) * E: MAKQUA Create quality control boxes file ADDQUA Add two quality control boxes ADLQUA Add all quality control boxes in one file GETQUA Read a quality control boxes file TABQUA Show one box at the terminal GRAQUA Contour one box in MOL-items CATQUA Put center atoms of boxes at the screen ALLQUA Does quality control on one molecule STBQUA Statistics about one box STSQUA Statistics about all boxes PARAMS Brings you in the QUALITY parameter menu SHOPAR Displays QUALITY related parameter values DRGQUA rotamer quality control RNGQUA does quality control on a residue range MUTQUA tries all mutants for a range E: HIDE01 Write formatted quality control boxes HIDE02 Convert formatted boxes to unformatted HIDE03 Do quality control over a list of files * * REFINE module messages * E: REFI Performs the regularization 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 your protein NOFIX Removes all FIX flags FIXCA Fixes all alpha carbons, de-fixes the rest ANCHOR Switches the ANCHOR option on NOANCH Switches the ANCHOR option off PARAMS (Re-)sets the regularization parameters * * SCAN3D module messages * E: 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 SCNSTS Brings you to menu to do statistics on groups SHOENT Go to menu to inspect database tables 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 * E: 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 INDEX Show database index NOW As INDEX, but give a bit more information SEQINF Show sequence information for one entry SHOHED Show the PDB file header for a database entry * * SCAN3D STATS messages * E: 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 * E: 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 * E: 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 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. ROWSTS Performs statistics on search results (counts hits) 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 ROW1TO 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 * E: 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 MOTIVS 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 STATS Gives fit statistics ISBEND Find the point of bending in case of domain bending PARAMS Brings you to the suppos parameter setting menu * * TABLES module messages * E: 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 TABRES Restores all table relevant data from a file TABACC Makes a table of residue 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 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 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 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 * E: 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 * E: GETCMC Sort the BIGFILE according to the sequence order in CMC file MAKCMC Write a CMC file that corresponds to the BIGFILE SRTCMC Sort a CMC file according to the CMC code MAKTFF MAKPTF 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 CORAN2 CORPM1 CORPM2 CORGR1 GETTIT As GETCMC, but also reads new titles from the CMC file * * WALGRA related messages * E: GRASQS Display sequences graphically SEQCOL 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 PRETYB As PRETYG, but black and white postscript PRETYC As PRETYB, but in colour * * WALIGN messages * E: WALCOR Activates the mutation correlation menu WALGRA Activates the graphical sequence menu WALPRF Activates the sequence profile and alignment menu WALSDB Activates the internal database 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 SHOMAT 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 REDUCE Put unique subset of sequences up front in BIGFILE HIDDEN Display `hidden` options PARAMS Brings you in the alignment parameter menu *WALHID E: HIDE01 Graphical display of pairwise similarities HIDE02 Read sequences from LFK style file HIDE03 Over-rule profile gap penalties with those from PARAMS HIDE04 Reads sequences from LFK-daily-update-files HIDE05 Checks if the Brh aligned sequences have the GPCR fingerprint HIDE06 Reserved for future use HIDE07 Delete sequences that do not have the GPCR fingerprint HIDE08 Does the whole 7TM HSSP process for one molecule class HIDE09 Reads sequence(s) from set of combines swissprot files HIDE10 Delete DNA sequences from the BIGFILE HIDE11 Read sequences from a `list2seq` file (alternative FASTA) HIDE12 Delete fragments from the BIGFILE HIDE13 Cluster sequences after alignment HIDE14 List WALIGN related common parameters and values HIDE15 Creates the file PDB.LIS HIDE16 Searches for decamers that can be good PCR probes HIDE17 Writes unaligned sequences as single records in a file HIDE18 As HIDE08, but including gap penaltie updates HIDE19 Reads sequences back that were written with HIDE17 HIDE20 Copies a bunch of SwissProt file local HIDE21 Searches in sequences for a fragment of requested weight HIDE22 Writes aligned sequences as single records in a file HIDE23 HIDE24 Runs all sequences against all profiles * * WALPRF messages * E: GETPRF Reads a profile from a file DELPRF Deletes a profile from the BIGFILE MAKPRF Writes a profile in a profile-file LSTPRF Lists the sequence information of a profile SHOPRF Lists all information of a profile ALIPRF Aligns sequences against a profile UPDPRF Updates a profile after alignment NEWPRF Makes a new profile from (aligned) sequence(s) 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 * * WALSDB messages * E: PREPDB Prepare the FASTB database FASTB This is the WHAT IF equivalent of FASTA DBPROF Run a profile against the whole database LSTSWP List one swissprot file GENPRF Runs a profile against a FASTA type file GENTST Runs a .NAM file against a FASTA file * * WALSEQ messages * E: 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 MAKINT Write sequence(s) in WHAT IF's formatted format GETINT Read sequences back from a WHAT IF format formatted file * * WALSRT messages * E: 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 * * WALSRV messages * E: GPCINI Initialize the big server file GPCOPE Open the existing big server file GPCSTS Show some 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 th profiles to classify the sequences GPCMAL Loop over all classes and make HSSP, MSF, etc. SER001 Create database per class from part of 7trmlist.txt SER002 Create multiple sequence alignment directory SER003 Show index of the internal database SER004 SER005 Creates local swissprot copies that are fully indexed SER007 Creates the central lines for a MODEL.html file SER008 Copies 7tmrlist.txt files to the local directory SER009 Reads DE and AC from files in FILES.LIST SER012 Creates directory structure * * XRAY related messages * E: EVADEN Convolutes bell shaped atoms with the density map EVACAS As EVADEN, but for alpha carbons only DETSEQ Determine sequence and structure correspondence FBRSYM Applies symmetry matrices to the FBRT object EXPSYM Applies symmetry matrices to a MOL-object 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. * * MAIN module messages * E: 3SSP Go to 3SSP menu ALLHEL Make entire secondary structure determination helix ANATRA Go to trajectory analysis menu APROPO Get writeup in hypertext window ACCESS Go to accessibility menu AUTOON Toggle command logging in script file on AUTOOF Toggle command logging in script file off ANACON Go to contact analysis menu BUILD Go to (ab initio) building menu CHIANG Go to torsion angle manipulation menu CENXYZ Send an arbitrary centering command to the graphics screen CHKMDF Go to H,K,L,F file inspection menu CONOLY Go to Connolly programs interface CLUFAM Go to cluster and family menu CHESS Play chess with WHAT IF CHOOSE Select predefined ranges for future options CHARGE Put GROMOS charges on atoms CHECK Go to PDB-file verification menu COLOUR Go to colouring menu DUTCH Let WHAT IF continue in Dutch DGLOOP Go to DGLOOP menu (rotamers, loop seraches) DIST Calculate distance between two atoms DEMOS Start the demonstration option DIRECT Toggle direct action graphics mode on DOLOG Switch on the result logging option DEBALL Debump multiple residues DEBHBO Debump residues, looking also at H-bonds DEBTRS Debump residues by translations of whole residues DRUG Go to drug (design) menu DEBUMP Debump one residue EDTHST Manually interfere with secondary structure determination END Brings you back to the previous menu EXTRA Go to the (experimental) protein folding menu ENGLIS Let WHAT IF continue in English ESSDYN Go to essential dynamics menu FULLST Terminate execution of WHAT IF GRID Go to GRIN/GRID interface menu GO Pass program control to the graphics window GRATWO Go to the menu for two dimensional graphics GROMOS Go to the GROMOS interface menu GETDSP Read C-alpha coordinates from a DSSP file GETMOL Read a PDB file GETMLS Read a list of PDB files GETGRO Read a GROMOS coordinate file GRAFIC Go to the main graphics menu GRAEXT Go to the menu for special graphics HELP Gives help about an option HISTOR Show the command history HSSP Go to the HSSP menu HBONDS Go to the hydrogen bond menu HYDMOM Go to the hydrophobic moment calculation menu E: INFO Gives extensive information about an option LABEL Go to the atomic labelling menu LISTA List atomic information for a residue (range) LISTR List the residue level information for a residue range LISTRR List the names and numbers of residues MAP Go to the (electron density) map menu MASMAP Go to the map massage menu (mainly for X-ray) MAPEDT Go to the enveloppe map editor menu MUTATE Mutate one residue MUTZON Mutate all residues into one same residue type MAKSCR Get demo script for ab initio building in present directory 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 MINMAX Determine extremes of a residue range MORE Increases in meny menus the number of options MYMENU Activates your menu (if you made one) NMR Go to the NMR menu NEWRNG De-activates the CHOOSE selected ranges NEWMOD Activates WHAT IF version 5.0 (bugged) OLDMOD Deactivates version 5.0 NEURAL Go to the neural network menu NEWHST Redetermine the secondary structure NOTES Go to notebook menu NOLOG Switch off result logging option PLOTIT Go to the plot menu PIRPSQ Go to the sequence operation menu (soon obsolete) PORNO Go to the molecular pornography menu QUALTY Go to the packing quality control menu RENUMB Renumber residues REFINE Go to the structure regularization menu SIMPLE Switch the automatic MOL-object/item administration on/off SUPPOS Go to the structure superposition menu SETPAR Go to the parameter setting menu SETWIF Change an internal program parameter SETICO Change a configuration parameter SPCIAL Go to the SPECIAL menu SEARCH Go to the parameter correlation row menu SELECT Go to the protein level menu of the relational database E: STYPEA Debug. Show type-ahead parameters SYMTRY Go to the symmetry menu SOUP Go to the soup menu SHORT Gives short help about all options in a menu SHORTT Give short help about all general options SHOHST Show the present secondary structure SETVDW Go to the Van def Waals radius editing menu SEQ3D Go to the menu from which the database is generated SCAN3D Go to the relational database menu SCRIPT Execute a script file START Read crambin from the internal database TRAROT Translate and rotate residue ranges TABLES Go to the spread sheet menu SHELL Create a shell (extra window) WATER Go to the water manipulation menu WALIGN Go to the new sequence manipulation menu XRAY Go to the X-ray menu $ Prefix for operating system commands % Prefix for commands in another than the present menu ! (or .)Prefix for repetition of an old command > < Prefixes for renaming commands, using renamed commands * * Symmetry messages * E: 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 * * VDW module messages * E: 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 * E: CUTOFF Maximal distance to neighbour for nayb COLNAY Colour of .NAYB lines to neighbours LINCOL Colour of lines made with screen option .LINE AA1OR3 Amino acid output in 1 or 3 letter code flag INSFLG Amount of sequence output flag NBOFSQ Number of one special sequence VDWOVR Bump/contact distance between Van der Waals radii DFBFAC Default B-factor NEIFLG Neighbour contact calculation flag CYSCYS Do/don't use inter chain cys-cys bridges BFTRED B-factor that corresponds to red in COLBFT NEICON Use covalent neighbours in BUMP/CONTAC like options * * PARDG module messages * E: DGCERR Maximal Ca-Ca distance misfit allowed DGTERR RMS Ca misplacement allowed DGSHWT Maximal number of hits to be shown by DGSHOW DGMHIT Minimal number of hits to be acceptable 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 * E: 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 * E: 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 * E: HITBBF What to show of the hit itself? HITNAF What to show of the hits environment? CONTYP SCNCON on one residue or whole stretch? HITOUT Flag to determine where SCNGRN hits should go * * PARGRO module messages * E: 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 FIXCA Fix alpha carbons flag FIXFRC Force with which to fix alpha carbons LEVUSE Determines level of interaction BATCH Run jobs interactively, or send to batch TRAJEC Flag for writing trajectories or not TRASTP Number of MD steps per written trajectory HPLACE Determines how hydrogen positions are generated MDORSD Determines which type of dynamics is used. MDINIT Determines how the MD run is initialised. * * PARBLD module messages * E: 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 * E: 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 * E: LINTYP User defined or colour dependend line types * * PARHBO module messages * E: 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 LINTYP Mode for drawing hydrogen bonds * * PARHBO module messages * E: WINDOW Width of the window PROPTY Property type number ANGLE Repeat angle for moment calculation * * PARNEU module messages * E: TEMP Initial 'temperature' of the training TEMPER Maximal allowed deviation in TEMP LINEAR Toggles the linear mode of the net ON/OFF ROBUST Toggles between quadratic and robust errors SMOOTH Toggles between quadratic and cubic errors. * * PARTRA module messages * E: PCWHAT Determines what can all be picked in a trajectory * * PARACC module messages * E: 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 * E: MINLEN Minimal number of residues needed in a stretch in MOTIV 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 * E: NCYCS Number of cycles NITS Number of iterations per cycle ZSCO Desired maximal Z score on any parameter REVLEV Sophistication level of REFI FIXFRC Force by which FIXed atoms are pulled back * * PARGRE module messages * E: 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 * E: ALHY Hydrogen bonded hydrogen polariaability EFHY Number of electrons per hydrogen bonded hydrogen IHVA Energy parameter mode for hydrogen bonded hydrogen LEVL Level of output QQHY Charge of hydrogen bonded hydrogen VDHY Hydrogen Van der Waals radius SHOPAR List the values of the parameters PROJEC (Re-)set the project number 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 * E: 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 * * PARCOL module messages * E: LOWCOL Lower colour of a colour range (1-360) HGHCOL Higher colour of a colour range (1-360) * * PARCNL module messages * E: ANGLE Courseness of the triangulation of the surface RADIUS Radius of the probe used to define the surface * * 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
0 blue 60 purple 120 red 150 orange 180 yellow 240 green 360 blueWhen 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). WEIGTH(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). CHARGE(IAT) charge of IAT. (REAL).
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