# Steric A program to calculate molecule cone angles and solid angles as measures of molecule steric size Programmed by B. Craig Taverner Main menu options: file - file options molecule - molecule data operations symmetry - perform crystallographic operations calculate - perform calculations plot - plot graphs of profile results change - change molecule and general calculation settings view - view current molecule data and general settings help - help facility exit - exit from steric In most cases preceding the command with an '&' character will result in the required operation being performed on all data sets currently loaded. Any commands not recognized by steric are passed to the operating system shell from which steric was loaded, so one can list files, and edit data sets without having to leave steric. In the case where the shell command required is recognized by steric, prepend it with the '!' character to bypass steric's command interpreter. If this is not enough, see the "file shell" option. Using the '>' character as the first character on the line will result in the text output being redirected to the file which has it's name following that character. If no filename is given the output is directed at stdout. Any arguments passed to steric on the command line are passed to the file loader. If they are recognizable atomic data files, they are loaded. If they are command files (starting with "#steric") they are used for command input instead of the default "steric.ini". If more than one command input file is given on the command line, currently only the last one will be used. #f file These are the main molecule data input and output options: load - load molecule data save - save molecule data svas - save molecule data under different name shell - open an operating system shell #fl file load Enter the names of the files to be loaded as arguments. Any number of files can be loaded with the same command. The following file formats are understood: - command files containing normal steric commands starting with the line #steric will be executed. Control is returned to the console after completion of execution, unless, of course, the last command was "exit". - steric data files starting with the line 'STERIC ...' - Biograph data files starting with the line 'BIOGRF ...' - Alchemy files in *.mol format - Biosym files in *.car format - Biograph conformer trajectory files in ascii format. These files are only used in the "calculate conformer" command. - Schakal data files - Shelxl data files - CSDS GStat coordinate file (converted with 'calc coord frac') - Alchemy crystal data file - Xtal crystal data file. Only 'atom', 'symtry', 'latice' and 'cell' lines are understood. The Schakal, Shelxl, gstat cor, alchemy crystal and xtal files all have fractional coordinates. The Cartesian coordinates are calculated immediately on loading, but the fractional coordinates are retained for possible future symmetry operations (see the "symmetry" command). Whenever additional atoms are added by such symmetry commands, there Cartesian coordinates are immediately calculated. If a command is given the makes the symmetry operators invalid (eg. "change origin"), the fractional coordinates are discarded, and only the Cartesian coordinates are retained. The symmetry operators themselves are also removed from that particular data sets memory space. #fs file save Save the current molecule data in steric format. All calculated data are included. #fa file svas Save the current molecule data in steric format in specified file. All calculated data are included. #fe file shell Open an operating system shell. This option is only available on some operating systems. Generally any commands not recognized by steric are passed on to the operating system anyway. If there is a command you wish to use that steric also understands, then prepend it with the '!' character and steric will pass it too the operating system unhindered. #m molecule These are the main molecule data operations: view - view the current molecule contents (see "view molecule") next - make the next molecule in memory the current molecule previous - make the previous molecule in memory the current molecule goto - make particular molecule current kill - mark atoms, atom types or groups as unusable in calculations close - remove elements of the current molecule from memory #mv view molecule The steric parameters calculated, as well as the current atomic contents are displayed. #mn molecule next Make the next molecule in memory the current one. #mp molecule previous Make the previous molecule in memory the current one. #mg molecule goto Make a particular molecule in memory the current one. Enter the molecule name or number on the command line, or it will be prompted for. Note that if a molecule has a number for a name, and you ask for a molecule with that number it will find the one with the matching name. #mk molecule kill Remove the following from further calculations: atoms - particular atoms located by name or number types - all atoms of a particular type groups - all occurances of particular groups numbers - all groups of a given number or name restore - undo the affects of any of the above options #mka molecule kill atoms Disable particular atoms (based on name or number) from participation in further calculations. #mkt molecule kill type Disable all atoms of particular type from participation in further calculations. #mkg molecule kill atoms Disable all atoms of particular atomic groups from participation in further calculations. The groups are defined in the file steric.grp Note the group must be clearly defined as being bonded to the origin defining atom or the main atom (use 'molecule view' to check) before it is identifiable as a group. #mkn molecule kill number Disable all atoms of particular atomic group number from participation in further calculations. #mkr molecule kill restore Allow all atoms, excepting the origin defining atom, to be involved in further calculations. #mc molecule close Remove the following from memory permanently: atoms - particular atoms located by name or number types - all atoms of a particular type groups - all occurances of particular groups numbers - all groups of a given number or name molecule - the entire molecule If the command is followed by strings that are not recognized as one of these options, then the strings are matched to group names, and any molecule not containing all requested groups is closed down. For example, "molecule close water perchlorate" will remove from memory all molecules not containing defined water and perchlorate groups. #mca molecule close atoms Delete particular atoms (based on name or number) from memory. #mct molecule close type Delete all atoms of particular type from memory. #mcg molecule close atoms Delete all atoms of particular atomic groups from memory. The groups are defined in the file steric.grp #mcn molecule close number Delete all atoms of particular atomic group number from memory. #mcm molecule close molecule Close the current molecule data. Memory is deallocated. #s symmetry These operation are only valid for molecular data for which the fractional coordinates have been provided. This allows the program to perform the symmetry transformations provided in the data files, or by the user. The following operations can be performed: transform - perform a single symmetry transformation expand - expand data with current symmetry box - expand data into predefined box of unit cells bond - find all bonds in current data group - find individual bonded molecular groups redundant - remove redundant atoms exclude - exclude atoms outside group cavities shell - use a radial profile to find the cavity radius volume - calculate specific crystal volumes #st symmetry transform A symmetry operator in the format used by the international tables can be given on the command line or will be prompted for. All atoms will have their fractional coordinates modified by this operator, and then have their Cartesian coordinates recalculated. #sx symmetry expand All symmetry operators present are used to generate an expanded data set. The original data is not overwritten, and nothing is done to ensure the data are all in the same unit cell. Any symmetry generated copies of atoms on special positions are removed. If the space group is centrosymmetric the inversion centre is first used to generate a double sized data set. This is then operated on by the other symmetry operators to generate a larger non-centred data set. Any centring operators present are then used to generate the full centred unit cell. #sb symmetry box Pure unit cell translational symmetry is used to expand the current data into the predefined box of unit cells. Any concurrent identical atoms are removed. The size of the box is defined by one to six numbers on the command line. If none are given a single unit cell is assumed. If three are given a box from 0,0,0 to the three in units of cell dimensions is created. If they are negative the box is made from the negative values to the positive values. If more than three are given, the first three represent the minima, and the last three represent the maxima. If only one is given three are assumed equal. For example "symmetry box -2" will box from [-2,-2,-2] to [2,2,2] and "symmetry box -1 0 2 3 4 5" will box from [-1,0,2] to [3,4,5]. #sd symmetry bond Find all bonds in current data. This algorithm uses the covalent radius of the atoms to determine the existence of bonds. The bond is determined to exist if the distance between the atoms is between two fractions of the radius, one larger than the radius and one smaller. See 'change settings bonding' for modification of these parameters. #sg symmetry group Search for bonded molecular groups in the current data set. All individual bonded molecules are assigned separate group numbers, and matched against the predefined groups in the steric.grp file so that they can be easily identified later. #sr symmetry redundant Remove any redundant atoms that are present from boxing atoms on special positions. See "change settings mode" for automating this. #se symmetry exclude This option is present for the purpose of speeding up the "symmetry volume group/cavity" calculations. The name of a group, or group type is specified on the command line, and all atoms not overlapping the group volume radius defined for that group (see "change molecule group") or for at least one matching group, are not only excluded from further calculations but removed from memory entirely. This dramatically speeds up the crystal calculations which can sometimes involve many thousands of unimportant atoms. Note that further calculations that require the entire data set will involve the reloading of the data. #ss symmetry shell This option is used to find the radial size of the cavity in which a defined group is present. The third argument on the line defines the required steric parameter to be used, and can be one of the following: oldleach - the solid angle calculated using the original Leach algorithm ryan - the solid angle calculated using the Ryan/Leach multiple overlap algorithm craig - the solid angle calculated using the Craig multiple overlap algorithm vertexO - the sum of all vertex angles of overlap between all pairs of atoms solidO - the sum of all solid angles of overlap between all pairs of atoms (see "calculate total ..." for further details on each one). Any further arguments describe the groups of interest. This calculation moves the origin to the main atom of the required group, and so any data sets that have fractional coordinates loose the use of those coordinates, as well as any symmetry operators present. The technique used involves the calculation of the radial profile (see "calculate profile") of the data set centred at the required group, and excluding that group, so as to get the steric profile of the group cavity. A cutoff steric value (see "change settings accuracy") is used on a smoothed profile (see "change settings size") to determine the radius at which the cavity ends. This radius is used to calculate a spherical cavity volume and is stored for possible use in the normal cavity volume calculation (see "symmetry volume cavity"). Note: If the radial profile never reaches the specified cutoff value, then the radius at the maximum profile value is used. #sv symmetry volume Certain crystallographically interesting volumes can be calculated: free - the free volume in the unit cell group - the volumes of all groups that match the named groups cavity - the volume of the cavity occupied by named groups #svf symmetry volume free The volume of all unoccupied space in the unit cell is calculated. #svg symmetry volume group All groups named on the command line are searched for and the volume of each instance found is calculated. #svc symmetry volume cavity The volume of all named groups in the command line is calculated in terms of it's cavity volume. This means that the volume of a predefined sphere around the group is calculated excluding all space occupied by groups other that the group of interest. See the "steric.grp" file for definition of the enveloping sphere. #c calculate There are currently three sets of calculations possible total - calculate the total value of the specified steric parameter conformer - calculate the conformer averaged value of the specified steric parameter profile - calculate the profile of the specified steric parameter volume - the molecular volume is calculated in cubic angstroms area - the molecular area orthogonally projected onto a plane volume - the molecular volume is calculated in cubic angstroms area - the molecular area orthogonally projected onto a plane #ct calculate total The following steric parameters can be calculated as a total value for the entire molecule #cc calculate conformer The following steric parameters can be calculated and averaged over all molecular conformers in the relevant ASCII trajectory file (extension '.trj') #cp calculate profile The following steric parameters can be calculated as radial profiles The cone angle can have it's angular profile calculated as well At the end of the calculation, the maximum value reached, as well as the area under the curve are output. #p plot Seven plots can be performed: orthog - orthogonal view of atomic outlines molecule - perspective view of atomic outlines cartesian - any profile is plotted on cartesian axes polar - any profile is plotted on polar axes steric - the results of particular steric calculations are output for all molecules contour - the contour data from the numerical solid angle calculation are plot using the external script 'contplot' profile - the radial profile contour is plotted in three dimensions #pn plot contour The contour data from the numerical solid angle are plot using the script 'contplot'. The molecule can be rotated about the z axis by a specified angle (see 'change settings rotation'). If the numerical solid angle profile calculation is done, the plot should represent the surface of the molecule. In both the total and the profile calculations the data are plot in three dimensions. The plot can be done in two modes: perspective (atoms further from the origin are reduced in size) and cartesian (true cartesian coordinates are used, all atoms are sized correctly). #po plot orthogonal An orthogonal view of the outlines of all atoms in the current molecule is plotted for the purpose of observing the nature of the overlaps involved. This is particularly useful for the analytical area calculation. #pm plot molecule A perspective view of the outlines of all atoms in the current molecule is plotted for the purpose of observing the nature of the overlaps involved. This is particularly useful for the multiple overlap solid angle calculation (see "calculate total craig"). #pc plot cartesian The following steric parameter profiles are plotted on cartesian axes. #pp plot polar The following steric parameter profiles are plotted on polar axes. #cp pc pp angular - the angular profile of the semi-vertex angle of the molecule about the origin-main atom bond direction #ct cc cp pc pp tolman - the tolman cone angle of the molecule cone - the maximum vertex angle of the molecule oldleach - the solid angle calculated using the original Leach algorithm ryan - the solid angle calculated using the Ryan/Leach multiple overlap algorithm craig - the solid angle calculated using the Craig multiple overlap algorithm numerical - the numerical solid angle calculated using the cone angle angular profile algorithm vertexO - the sum of all vertex angles of overlap between all pairs of atoms solidO - the sum of all solid angles of overlap between all pairs of atoms #ct cc volume - the molecular volume is calculated in cubic angstroms #ct cc pc pp area - the molecular area orthogonally projected onto a plane #ctt cct cpt pct ppt The Tolman Cone Angle: This is calculated based on the groups defined during the loading of the data sets, or after any major change. If there is no origin defining atom, no groups are defined. If the origin defining atom has several bonds the the groups are defined as those molecular fragments bonded to the origin defining atom. If the origin defining atom has only one bond, then the atom bonded, called the 'main atom' has the groups defined about it, and it itself is allocated to the zero group. This last case is clearly useful for the calculation of the Tolman Cone Angle, which is simply the average of the cone angles of the groups present. If there are three or more groups about the 'main atom' then the zero group is not used in the Tolman cone angle calculation. If however, there are less than three groups bonded to the main atom, the zero group, which represents only the cone angle of the main atom itself, is also used in the tolman cone angle calculation, so that the cone angle still represents the steric 'distribution' about the main atom. #ctc ccc cpc pcc ppc The Cone Angle: This is calculated at the maximum vertex angle about the origin-main atom bong vector, and should correspond to the maximum value obtained in the angular profile calculation. It is calculated very simply as the theta angle of the atom with the greatest theta angle from the main atom bond (the bond from the origin defining atom to the ligand atom) plus it's semi-vertex angle, and then doubled to be consistent with the Tolman cone angle. #cto cco cpo pco ppo The Old Leach Solid Angle: This is the original algorithm used in the calculation of the molecule solid angles in the program "CONE". It involves summing the solid angles of pairs of atoms, followed by subtracting the extra single atom solids angles that result. This does not take into account the possibility of multiple overlaps of order three or above. In order to reduce this error, the counting of pairs of atoms has been done in a specific way to reduce the occurances of erroneous missing multiple overlaps. For many molecules this works quite well, but unfortunately it can be shown that, since not all possible double overlaps are taken into account, this algorithm very rarely gives the exact solid angle, excepting in the radial profile calculations, where multiple overlaps are relatively rare, or at least very small. In the case of total solid angles unfortunately, in no case but the simplest two atom data sets, can it be said for sure that the solid angle calculated will be exactly correct. An additional problem was found in the actual integration of the solid angle of two overlapping regions: due to the particular choice of origin, it occasionally occured that segments were left out of the calculation. The correction algorithm employed for this has since been shown not to be bug free, and therefore this correction is optional (see 'change settings mode'). An alternative to the original segment correction is the option to use one of the new features in the multiple overlap calculations to perform the correction (see 'change settings mode'). #ctr ccr cpr pcr ppr The Ryan/Leach Multiple Overlap Solid Angle In order to solve the problems that occur in the Old Leach Solid Angle due to it's not taking multiple overlaps of order higher than two into account, Peter Leach developed further equations for the calculations of solid angles of regions of multiple overlap. These were developed into an algorithm and coded by Ryan Lemmer. #ctg ccg cpg pcg ppg The Craig Multiple Overlap Solid Angle In order to solve the problems that occur in the Old Leach Solid Angle due to it's not taking multiple overlaps of order higher than two into account, Craig Taverner developed a set of vector based equations for the calculations of solid angles of regions of multiple overlap. These equations also replaced much of the maths used in the Old Leach Solid Angle algorithm, leaving only the equations for the ellipse parameters by Peter Leach. The Algorithm was developed and coded by Craig Taverner. #ctn ccn cpn pcn ppn The Numerical Solid Angle This is calculated simply by integrating over the angular cone angle profile. The cone angle values at all phi angles can be output to a file for use in molecular contour plots (see 'change settings mode'). Currently there is a bug in the code which results in most solid angles being overestimated in all but the highest symmetry cases. This will be resolved as soon as possible. #ctv ccv cpv pcv ppv The Vertex Angle of Overlap This is the sum of all the vertex angles of the overlap regions found between all overlapping pairs of atoms. It can be used as a means of estimating steric congestion. It's main advantage is in the simplicity of the calculation: VAO = alpha + beta - chi Using the non-bonded overlap option (see "change settings mode"), only non-bonded interactions are taken into account. Using the no inter-group overlap option (see "change settings mode"), only interaction between atoms of different groups are taken into account. See "calculate total tolman" for a description of the group definitions. #cts ccs cps pcs pps The Solid Angle of Overlap This is the sum of all the solid angles of the overlap regions found between all overlapping pairs of atoms. It can be used as a means of estimating steric congestion. It is not as simple as the vertex angle of overlap calculation because it uses calculations from the Craig multiple overlap algorithm, but is a more quantitative measure of steric overlap. It is intended for future versions to give the solid angle of the total region of overlap as opposed to the current simple sum. Since this will count all orders of overlap as equal, it will only be implemented as an option, because the current version clearly gives a greater emphasis on multiple overlap. This is considered desirable. Using the non-bonded overlap option (see "change settings mode"), only non-bonded interactions are taken into account. Using the no inter-group overlap option (see "change settings mode"), only interaction between atoms of different groups are taken into account. See "calculate total tolman" for a description of the group definitions. #cv ctl ccl The molecular volume This calculation is a simple numerical calculation of the volume of the molecule. Two methods are provided: 1 - A box enveloping the entire molecule is divided into a three dimensional grid and then all elements of the grid that are within the molecule have their volumes added to the total. See 'change settings volume' for help on modifying the grid. 2 - Monte Carlo approach in which the points inside the box are sampled at random, and the molecular volume calculated from the ratio found inside the molecule. See 'change settings volume' and 'change settings accuracy' for relevant settings. #ca ctp ccp The orthogonally projected molecular area This calculation is a fully analytical calculation. Firstly the entire molecule is orthogonally projected onto a plane, by default the xy plane. It then uses a procedure similar to that used in the multiple overlap solid angle calculation (see "calculate total craig") to cut the molecular projection up into sections representing single atoms, regions of overlap of two atoms, regions of triple overlap, regions of quadruple overlap, etc. up until either no higher order of overlap exists in the particular data set, or the maximum level of overlap allowed is reached. The default for this is 10. The total area is calculated analytically by summing the areas of all odd orders of overlap, including single atoms, and subtracting all even orders. Each region of multiple overlap has its area calculated using simple trigonometric formulae to decompose the region into subregions of segments of circles and simple triangles. With no arguments this command calculates the area of the molecular projection onto the plane defined in "change molecule plane", or (0,0,1) (ie. xy plane) if not defined. For more complex calculations the following arguments can be given: theta - projected areas verses a range of theta rotations of the plane phi - projected areas versus a range of phi rotations of the plane map - projected areas versus both theta and phi rotations #cat calculate area theta The plane of projection is rotated stepwise (see "change settings size") through the theta range specified in "change molecule plane" from the defined position, and the projected area onto the plane at each step is calculated and stored in the profile array (see "plot cartesian area" and "plot polar area"). #cap calculate area phi The plane of projection is rotated stepwise (see "change settings size") through the phi range specified in "change molecule plane" from the defined position, and the projected area onto the plane at each step is calculated and stored in the profile array (see "plot cartesian area" and "plot polar area"). #cam calculate area map The plane of projection is rotated stepwise (see "change settings size") through both the theta and phi ranges specified in "change molecule plane" from the defined position, and the projected area onto the plane at each step is calculated and stored in the profile array (see "plot cartesian area" and "plot polar area"). #a change The folling data can be modified molecule - current molecule data settings - the general calculation settings origin - origin for all cone and solid angle calculations parameter - the data in the atomic parameter table #am The following molecular parameters can be changed group - group specific data plane - plane onto which projections are made #amg change molecule group The cavity volume radius and the groups aliases can be changed #amp change molecule plane Up to 10 arguments can be given. If any are omitted, they are left unchanged. All arguments will be read as double precision floating point numbers and mean the following: 1 to 3 - vector defining perpendicular to plane (z in plane system) default (0.0,0.0,1.0) in normal coordinates 4 to 6 - vector defining phi=0 in plane system (x in plane system) default (1.0,0.0,0.0) in normal coordinates 7, 8 - minimum and maximum values of theta for rotation of plane default 0 and PI 9, 10 - minimum and maximum values of phi for rotation of plane default 0 and 2*PI The "calculate area" command uses only the plane defining vector to calculate the area of projection onto. The "calculate area theta" command uses both vectors and the theta range to calculate the projected area over a one dimensional range. The "calculate area phi" command uses both vectors and the phi range to calculate the projected area over a one dimensional range. The "calculate area map" command uses both vectors and both ranges to calculate the projected area over a two dimensional range. All three maps are stored in the one dimensional array used for double precision array storage. None can be in memory simultaneously. #as change settings The settings of the following can be changed order - change maximum order of multiple overlap considered in Craig multiple overlap solid angle calculations range - the general angular and radial profile ranges rotation - the contour plot rotation size - the profile array sizes, and the size of the numerical solid angle integration array mode - the general calculation modes are changed accuracy - the maximum error in the leach algorithm calculations, and the Monte Carlo volume plot - the parameters for the molecule plot volume - the grid used in the numerical volume calculation bonding - the settings used in the bond search can be changed #asm Several settings can be changed: - The profile ranging mode can be set so that the profile ranges are either taken from the general settings range, or from the individual molecule ranges. - The improved G positioning feature used in the Craig and the Ryan solid angle calculations can be set to be used in the Oldleach solid angle calculation as well. - The oldleach solid angle calculation can be set to either use the segment correction algorithm or not. The default is not to use it, because it was found to be inaccurate. - The vertex angle of overlap and solid angle of overlap calculations can be set to consider only overlaps occuring between non-bonded atoms. - The vertex angle of overlap and solid angle of overlap calculations can be set to consider only overlaps occuring between atoms in different groups. - The numerical solid angle calculation can be set to output the angular-radial contour data involved. - The contour plot can be set to perspective mode. - van der Waals radii can be used in all calculations. - the Monte Carlo method can replace the default fixed grid in volume calculations. - dummy unit cell atoms can be allowed to be visible to the "view molecule atoms" command. - the unit cell can be automatically boxed in the group and cavity volume calculations. #ao change origin The origin can be changed in three ways: atom - the atom defining the origin can be changed group - the origin can be changed to the main atom of a group distance - the origin distance from the main atom can be changed #aoa change origin atom Entering either the origin atom name or number as an argument will result in all atomic coordinates changing to place that atom at the origin. All distances and semi-vertex angles are recalculated. The new origin atom is marked to be excluded from further calculations. The groups present are reassigned. #aoa change origin group Entering either the group name or number as an argument will result in all atomic coordinates changing to place that groups main atom at the origin. All distances and semi-vertex angles are recalculated. The new origin atom is marked to be excluded from further calculations. The groups present are reassigned. #aod change origin distance Entering a distance in angstroms as an argument will result in all atomic coordinates changing so as to move the origin to that distance from the main atom, along the vector direction from the main atom to the original origin. All distances and semi-vertex angles are recalculated. #ap change parameters The contents of the atomic parameter table can be modified. #v view the following data can be viewed molecule - atomic data of the current molecule parameter - the atomic parameter table settings - the current general calculation settings #vm view molecule This command can be given with the following arguments: atoms - The molecules atom list is displayed groups - The molecules group list is displayed symmetry - The molecules symmetry operator list is displayed In any case, even if no argument is given, the following is displayed: The steric parameters calculated, as well as the current atomic contents and group assignments are displayed. Steric Parameters: - The original tolman cone angle calculated when the data set was loaded. If you have modified the group assignments this is likely to no longer be the correct value. Use "calculate total tolman" to find the correct value. - The total value, conformer average, maximum profile and profile area are displayed for all steric calculations. Group Assignments: - The groups found for the current molecular configuration are listed. If a zero group exists, it is because the groups are defined about the main atom bonded to the origin defining atom, and this atom has been assigned to the zero group for special Tolman cone angle calculations (see "calculate total tolman"). The semi-vertex angles in each case are used for the Tolman cone angle calculations. #vma view molecule atoms All the important parameters pertaining to the atoms present are listed. This includes number, group, position (cartesian and polar), radius and semi-vertex angle. The origin defining atom is indicated with a 'o' character, and the main atom with a '*' character. The semi-vertex angle present is the one last used in a calculation, and therefore may change (eg. in the profile calculation the semi-vertex angle changes constantly). #vmg view molecule groups The listing of individually defined groups is given. Groups are defined either as separate molecules, or as separate ligands bonded to the origin defining atom, or as individual branches on the ligand if only one ligand is present. #vms view molecule symmetry The list of symmetry operators loaded with the current molecule is displayed. Normal symmetry is listed as "SYMM" while centring conditions are listed as "CENT". #vp view parameters The contents of the atomic parameter table are displayed. This table currently contains only the van der Waals and covalent radii found in the 'steric.par' file. #vs view settings The current general settings are displayed. #h help Help can be obtained on each command by entering that command as an argument after help. for example: help file - gives help on the file options help file load - gives help on the file loading option All commands are also associated with single characters, most often the first character of the command. for example: 'help file load' can be replaced with 'h f l'. The spaces are obligatory. When more than one command in the same menu level starts with the same character, another character from the word has been assigned as the shortcut character. for example: 'calculate total craig' is 'c t g' #x exit Exit the steric program #mkg mkn mcg mcn The groups are defined by their numbers (or names). Note the group must be clearly defined as being bonded to the origin defining atom or the main atom (use 'molecule view' to check) before it is identifiable as a group.