## ## filename: ## MANUAL.txt ## ## description: ## This file is used by the program PDBMANAGER v 1.0 to output help information ## on specified topics on the screen. Although this file is named as ## MANUAL.txt, it is actually not the real manual for the PDBMANAGER. ## The PDBMANAGER manual is stored in the file PDBMANAGER_V10_USER_MANUAL.pdf. ## HELP Command help provides help on a given topic. Usage: help Topic is one of the following: Commands: command atmo command bc command calc command cat command cd command chmod command clear command commandfile command convert command cp command cryst command date command def command del command dir command edit command empty command exit command expr command find command getenv command getmemory command help command isdef command isempty command isvalid command load command ls command math command millisleep command mkdir command move command mv command povray command print command pwd command quit command rand32 command rand64 command rename command reset command richtext command rm command rmdir command save command select command selected command set command setenv command sleep command str command strvec command symmetry command sysinfo command thread command timer command touch command var command version command which command view command viewobj command voronoi Special keys: key arrow down key arrow left key arrow right key arrow up key backspace key delete key end key f1 key f2 key f3 key f4 key f10 key home key page down key page up key return END_HELP KEYS KEY: arrow down DESCRIPTION: Browses the command history forwards. END_KEY KEY: arrow left DESCRIPTION: Moves cursor on the input control to the left. END_KEY KEY: arrow right DESCRIPTION: Moves cursor on the input control to the right. END_KEY KEY: arrow up DESCRIPTION: Browses the command history backwards. END_KEY KEY: backspace DESCRIPTION: Deletes the character located left of the cursor. END_KEY KEY: delete DESCRIPTION: Deletes the character under the cursor. END_KEY KEY: end DESCRIPTION: Scrolls the screen to the end of the line history. END_KEY KEY: f1 DESCRIPTION: Scrolls output control to first line. END_KEY KEY: f2 DESCRIPTION: Scrolls output control to last line. END_KEY KEY: f3 DESCRIPTION: Scrolls output control up one page. END_KEY KEY: f4 DESCRIPTION: Scrolls output control down one page. END_KEY KEY: f12 DESCRIPTION: Clears output control. END_KEY KEY: home DESCRIPTION: Scrolls output control to first line. END_KEY KEY: page down DESCRIPTION: Scrolls output control down one page. END_KEY KEY: page up DESCRIPTION: Scrolls output control up one page. END_KEY KEY: return DESCRIPTION: Executes the current command. END_KEY COMMANDS COMMAND: atmo DESCRIPTION: Used to handle AtomicModel objects USAGE: atmo calc all (Calculates some parameters describing AtomicModel) atmo get atom_coord int1 (Gets atom int1 coordinates and stores them to Str var) atmo get cm_all (Stores the centre of mass of all coordinates in Atmo var to Str var) atmo get cm_selected (Stores the centre of mass of selected coordinates in Atmo var to Str var) atmo get cm_unselected (Stores the centre of mass of unselected coordinates in Atmo var to Str var) END_COMMAND COMMAND: bc DESCRIPTION: Executes the unix/linux command bc. USAGE: bc -all arg1 ... argN (Outputs the result from bc with arguments arg1 ... argN to screen and to varible String variable. If args are String variables then their values are used.) bc -scr arg1 ... argN (Outputs the result from bc with arguments arg1 ... argN to screen. If args are String variables then their values are used.) bc -str arg1 ... argN (Stores the result from bc with arguments arg1 ... argN to String variable. If args are String variables then their values are used.) END_COMMAND COMMAND: calc DESCRIPTION: Calculates different functions from AtomicModel variable. USAGE: calc debyeint all double1 int1 (Calculates debyeint for all atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) calc debyeint selected double1 int1 (Calculates debyeint for selected atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) calc debyeint_tab1 all double1 int1 (Calculates debyeint for all atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) calc debyeint_tab2 selected double1 int1 (Calculates debyeint for selected atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) calc debyeint_tab1 all double1 int1 (Calculates debyeint for all atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) calc debyeint_tab2 selected double1 int1 (Calculates debyeint for selected atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) calc fourierint all double1 int1 int2 (Calculates debyeint for selected atoms in the AtomicModel variable double1 is maximum value, int1 is number of points in the function and int2 is the number of points in p(r)-function used for transformation to intensity.) calc fourierint selected double1 int1 int2 (Calculates debyeint for selected atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function and int2 is the number of points in p(r)-function used for transformation to intensity.) calc pr all double1 int1 (Calculates p(r)-function for all atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) calc pr selected double1 int1 (Calculates p(r)-function for selected atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) END_COMMAND COMMAND: cat DESCRIPTION: Unix/linux system command for concatenate files and print on screen. USAGE: Same as unix/linux command. END_COMMAND COMMAND: cd DESCRIPTION: Modified Unix/linux system command for changing directory. Currently accecpts . .. and ~ at the begining of command. Multiple ..'s are not allowed (i.e. ../..). One may use String variable as first argument. USAGE: cd arg1 ... argN (Changes the directory to 'arg1 ... argN') cd arg2 ... argN (Changes the directory to String variable + 'arg2 ... argN') REMARKS: See the file cd_ex1.cmd for further information. END_COMMAND COMMAND: chmod DESCRIPTION: Unix/linux system command for changing file access permissions. USAGE: Same as unix/linux command. END_COMMAND COMMAND: clear DESCRIPTION: Clears all the varibles from the memory. USAGE: clear REMARKS: Notifies if no variables were defined. END_COMMAND COMMAND: commandfile DESCRIPTION: Reads PDBMANAGER commands from the file given as parameter. USAGE: commandfile filename (Reads PDBMANAGER commands from the file filename and passes them straight to executeCommand-function. No mark of commands is left to commandline history) commandfile -exec filename (Reads PDBMANAGER commands from the file filename and passes them to COMMAND_KEY_RETURN-function. Commands will be saved to commandline history) END_COMMAND COMMAND: convert DESCRIPTION: Converts pdb- and xyz-formats to xyzdat-format and vice versa (if possible) USAGE: convert dat_to_xyz all (Converts all cordinates from the xyzdat-file given in Str var1 to xyz-file given in Str var2) convert dat_to_xyz all (Converts all cordinates from the xyzdat-file given in Str var to xyz-format AtMo var) convert dat_to_xyz lines int1 int2 (Converts cordinates from lines int1 to int2 int the xyzdat-file given in Str var1 to xyz-file given in Str var2) convert dat_to_xyz lines int1 int2 (Converts cordinates from lines int1 to int2 in the xyzdat-file given in Str var to xyz-format AtMo var) convert dat_to_xyz_append all (Converts all cordinates from the xyzdat-file given in Str var1 and appends to xyz-file given in Str var2) convert dat_to_xyz_append all (Converts all cordinates from the xyzdat-file given in Str var and appends it to xyz-format AtMo var) convert dat_to_xyz_append lines int1 int2 (Converts cordinates from lines int1 to int2 int the xyzdat-file given in Str var1 and appends to xyz-file given in Str var2) convert dat_to_xyz_append lines int1 int2 (Converts cordinates from lines int1 to int2 in the xyzdat-file given in Str var and appends to xyz-format AtMo var) convert xyz_to_dat all (Converts all coordinates (in all structures) from xyz-file format to xyzdat-file format). Str var2 is input file (xyz-file) and Str var1 is output file (xyzdat-file)) convert xyz_to_dat all (Converts all coordinates in AtMo var from xyz-file format to xyzdat-file format. Coordinates are stored in xyzdat-format to the file giiven in Str var1) convert xyz_to_dat selected (Converts selected coordinates in AtMo var from xyz-file format to xyzdat-file format. Coordinates are stored in xyzdat-format to the file giiven in Str var1) convert xyz_to_dat struct strIndexInt (Converts xyz-coordinates from structure strIndexInt in the file given in Str var2 to xyzdat-file format. Output file is given in Str var1 (xyzdat-file) convert xyz_to_dat_append ... (This option has exactly the same syntax as xyz_to_dat except the resulting structures are appended to given file (old content is left untouched) END_COMMAND COMMAND: cp DESCRIPTION: Unix/linux system command for copying file(s). USAGE: Same as unix/linux command. REMARKS: Doesn't currently support wildcards * ?. END_COMMAND COMMAND: cryst DESCRIPTION: Performs operations for crystal generators. USAGE: cryst add (add one crystal generator) cryst add int1 (add one base vector for crystal generator int1) cryst add int1 int2 (add int2 base vectors for crystal generator int1) cryst clear (Erases all crystal generators) cryst clear int1 (Erases all base vectors for crystal generator int1) cryst convert int1 xyz_to_abc (Converts point given in Str var2 from xyz representation to abc representation and stores the result to Str var2) cryst convert int1 abc_to_xyz (Converts point given in Str var2 from abc representation to xyz representation and stores the result to Str var2) cryst convert int1 abc_to_xyz (Converts points in Atmo var from abc representation to xyz representation) cryst convert int1 xyz_to_abc (Converts points in Atmo var from xyz representation to abc representation) cryst del int1 (Erases crystal generator int1) cryst del int1 int2 (Erases base vector int2 from crystal generator int1) cryst generate xyzfile int1 int2 int3 int4 ... (Generates Crystal to XYZ-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. The location of Atmo vars is fixed by moving their centre of masses to corresponding int1 CrystalGenerator base vector) cryst generate_abc xyzfile int1 int2 int3 int4 ... (Generates Crystal to XYZ-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. In this option it is assumed that AtMos are located and oriented correctly in abc-space in unit-cell) cryst generate_xyz xyzfile int1 int2 int3 int4 ... (Generates Crystal to XYZ-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. In this option it is assumed that AtMos are located and oriented correctly in xyz-space) cryst generate pdbfile int1 int2 int3 int4 ... (Generates Crystal to PDB-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. The created PDB-file uses header recors from the PdbData variable.) cryst generate_abc pdbfile int1 int2 int3 int4 ... (Generates Crystal to PDB-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. In this option it is assumed that AtMos are located and oriented correctly in abc-space in unit-cell. The created PDB-file uses header recors from the PdbData variable.) cryst generate_xyz pdbfile int1 int2 int3 int4 ... (Generates Crystal to PDB-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. In this option it is assumed that AtMos are located and oriented correctly in xyz-space. The created PDB-file uses header recors from the PdbData variable.) cryst generate_with_borders xyzfile int1 int2 int3 int4 ... (Generates Crystal to XYZ-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. In the begining of xyz-coordinates there is border atoms generated using xyz-format atom names stored in the StrVec variable. Atoms will be equili-distributed on the unit cell surfaces with number of atoms per dimension and face equal to number of elements in the StrVec variable.) cryst generate_borders xyzfile int1 int2 int3 int4 (Generates unit cell borders to XYZ-file given in the Str var1. There will be int2, int3 and int4 unit cells in x,y,z -directions. Unit cells are generated with CrystalGenerator with index int1 and comment from Str var2. Border atoms generated using xyz-format atom names stored in the StrVec variable. Atoms will be equili-distributed on the unit cell surfaces with number of atoms per dimension and face equal to number of elements in the StrVec variable.) cryst generate_oriented xyzfile int1 int2 int3 int4 ... (Generates Crystal to XYZ-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. In addition, every AtomicModel is oriented according to rotations by rotators with indexes given in the StrVec var. StrVec var must have same number of elements as base vector.) cryst generate_oriented pdbfile int1 int2 int3 int4 ... (Generates Crystal to PDB-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. The created PDB-file uses header recors from the PdbData variable. In addition, every AtomicModel is oriented according to rotations by rotators with indexes given in the StrVec var. StrVec var must have same number of elements as base vector.) cryst generate_oriented_with_borders xyzfile int1 int2 int3 int4 ... (Generates Crystal to XYZ-file given in the String variable. Crystal has int2, int3 and int4 unit cells in x,y,z -directions. Crystal is generated with CrystalGenerator with index int1 and AtomicModels stored in AtomicModels. If more than one AtomicModels are given then there must be as many AtomicModels specified than there is base vectors in the unit cell. If only one AtomicModel is given then all base vectors use it. In the begining of xyz-coordinates there is border atoms generated using xyz-format atom names stored in the StrVec var2. Atoms will be equili-distributed on the unit cell surfaces with number of atoms per dimension and face equal to number of elements in the StrVec variable. In addition, every AtomicModel is oriented according to rotations by rotators with indexes given in the StrVec var2. StrVec var2 must have same number of elements as base vector.) cryst print (Prints all crystal generators) cryst print int1 (Prints crystal generator int1) cryst set int1 id (Set id to String variable for crystal generator int1) cryst set int1 a double1 (Set a to double1 for crystal generator int1) cryst set int1 b double1 (Set b to double1 for crystal generator int1) cryst set int1 c double1 (Set c to double1 for crystal generator int1) cryst set int1 alpha double1 (Set alpha to double1 for crystal generator int1) cryst set int1 beta double1 (Set beta to double1 for crystal generator int1) cryst set int1 gamma double1 (Set gamma to double1 for crystal generator int1) cryst set int1 all double1 double2 double3 double4 double5 double6 (Set all lattice params (a,b,c,alpha,beta,gamma) for crystal generator int1) cryst set int1 base int2 double1 double2 double3 (Set base vector int2 for crystal generator int1) cryst set int1 all (Set all lattice params (a,b,c,alpha,beta,gamma) for crystal generator int1 from Str var. Params are given in Str var as double precision numbers separated by empty spaces) cryst set int1 base int2 (Set base vector int2 for crystal generator int1 from Str var. Params are given in Str var as double precision numbers separated by empty spaces) END_COMMAND COMMAND: date DESCRIPTION: Prints current date on the screen or to String variable. USAGE: date (Prints current date on the screen) date (Prints current date to String variable) END_COMMAND COMMAND: def DESCRIPTION: Defines variable of given class. USAGE: def REMARKS: Variable must be defined before it is used! All variables must have class specified! END_COMMAND COMMAND: del DESCRIPTION: Deletes the variable. USAGE: del ... REMARKS: Prints error message if variable was not defined. END_COMMAND COMMAND: dir DESCRIPTION: Unix/linux system command ls for printing the directory on the screen. USAGE: Same as unix/linux command. REMARKS: Doesn't currently support wildcards * ?. END_COMMAND COMMAND: edit DESCRIPTION: Starts text editor with the command given in the variable EDITOR_COMMAND. REMARKS: The variable EDITOR_COMMAND is located in the file ENVIRONMENT.txt and can be changed. NOTICE: If EDITOR_COMMAND command is not in your PATH variable you have to specify the whole path for the command (For instance, /usr/local/bin/emacs) Otherwise, it is sufficient to use the text editor name (For instance, emacs). END_COMMAND COMMAND: empty DESCRIPTION: Empties the variable. USAGE: empty var ... (Empties all the given variables) empty intensity (Empties k and intensity vectors in the given AtomicModel variable) empty pr (Empties r and pr vectors in the given AtomicModel variable) empty exp_intensity (Empties exp_k and exp_intensity vectors in the given AtomicModel variable) empty exp_pr (Empties exp_r and exp_pr vectors in the given AtomicModel variable) empty atomic_all (Empties all vectors in the given AtomicModel variable) END_COMMAND COMMAND: exit DESCRIPTION: Terminates the program. USAGE: exit REMARKS: Outputs the exit text. END_COMMAND COMMAND: expr DESCRIPTION: Executes the unix/linux command expr. USAGE: expr -all arg1 ... argN (Outputs the result from expr with arguments arg1 ... argN to screen and to varible String variable. If args are String variables then their values are used.) expr -scr arg1 ... argN (Outputs the result from expr with arguments arg1 ... argN to screen. If args are String variables then their values are used.) expr -str arg1 ... argN (Stores the result from expr with arguments arg1 ... argN to String variable. If args are String variables then their values are used.)x END_COMMAND COMMAND: find DESCRIPTION: Unix/linux system command for finding files. USAGE: Same as unix/linux command. END_COMMAND COMMAND: getenv DESCRIPTION: Gets the given environmental variable and prints it on the screen or stores it to String variable. USAGE: getenv ENVIRONMENTAL_VARIABLE (Prints the value of ENVIRONMENTAL_VARIABLE on the screen) getenv ENVIRONMENTAL_VARIABLE (Stores the value of ENVIRONMENTAL_VARIABLE to String variable) END_COMMAND COMMAND: getmemory DESCRIPTION: Prints the amount of free on the screen or to String variable. USAGE: getmemory (Prints the amount of free memory on the screen if available) getmemory (Prints the amount of free memory to the String variable. If information is not available then String variable is set to NULL) END_COMMAND COMMAND: help DESCRIPTION: Prints help text for a given topic. USAGE: help command help key REMARKS: List of the topics can be seen when started without arguments. END_COMMAND COMMAND: isdef DESCRIPTION: Prints on the screen is the variable defined or not. USAGE: isdef END_COMMAND COMMAND: isempty DESCRIPTION: Prints on the screen is the variable empty or not. USAGE: isempty END_COMMAND COMMAND: isvalid DESCRIPTION: Prints on the screen if the file is valid or not. USAGE: isvalid datfile (Is the file given in the String variable valid dat-file or not) isvalid pdbfile (Is the file given in the String variable valid pdb-file or not) isvalid xyzfile (Is the file given in the String variable valid xyz-file or not) isvalid xyzdatfile (Is the file given in the String variable valid xyzdat-file or not) END_COMMAND COMMAND: load DESCRIPTION: Loads variable(s) from the file. USAGE: load file int1 (Loads AtomicModel int1 from the file given in the String variable to AtomicModel variable) load file intensity (Loads AtomicModel variable from the file given in the String variable) load file pr (Loads AtomicModel variable from the file given in the String variable) load file exp_intensity (Loads AtomicModel variable from the file given in the String variable) load file exp_pr (Loads AtomicModel variable from the file given in the String variable) load file (Loads StringVector variable from the file given in the String variable) load file int1 int2 (Loads StringVector variable from the file given in the String variable. Lines from int1 to int2 are read from the file) load var (Loads all the PDBMANAGER variables from the file given in the String variable) load var variable1 ... variableN (Loads variables variable1 ... variableN from the file given in the String variable) END_COMMAND COMMAND: ls DESCRIPTION: Unix/linux system command for printing the directory on the screen. USAGE: Same as unix/linux command. REMARKS: Doesn't currently support wildcards * ?. END_COMMAND COMMAND: mkdir DESCRIPTION: Unix/linux system command for making directory. USAGE: Same as unix/linux command. END_COMMAND COMMAND: move DESCRIPTION: Moves the atoms in the AtomicModel variable. USAGE: move all double1 double2 double3 (Moves all atoms in the AtomicModel variable with vector (double1,double2,double3)) move selected double1 double2 double3 (Moves selected atoms in the AtomicModel variable with vector (double1,double2,double3)) move unselected double1 double2 double3 (Moves unselected atoms in the AtomicModel variable with vector (double1,double2,double3)) move amino int1 double1 double2 double3 (Moves atoms in the amino acid int1 in the AtomicModel variable with vector (double1,double2,double3)) move atom int1 double1 double2 double3 (Moves atom int1 in the AtomicModel variable with vector (double1,double2,double3)) move aminos int1 int2 double1 double2 double3 (Moves atoms in the amino acids int1 to int2 in the AtomicModel variable with vector (double1,double2,double3)) move atoms int1 int2 double1 double2 double3 (Moves atoms int1 to int2 in the AtomicModel variable with vector (double1,double2,double3)) move all (Moves all atoms in the AtomicModel variable with vector given in Str var) move selected (Moves selected atoms in the AtomicModel variable with vector given in Str var) move unselected (Moves unselected atoms in the AtomicModel variable with vector given in Str var) move all_to_cm (Moves all atoms in the AtMo var such that the centre of mass of whole AtMo var is at origo.) move selected_to_cm (Moves selected atoms in the AtMo var such that the centre of the mass of selected atoms is at origo) move unselected_to_cm (Moves unselected atoms in the AtMo var such that the centre of the mass of selected atoms is at origo) move all invertX (Inverts all x-coordinates in AtMo) move all invertY (Inverts all y-coordinates in AtMo) move all invertZ (Inverts all z-coordinates in AtMo) move selected invertX (Inverts selected x-coordinates in AtMo) move selected invertY (Inverts selected y-coordinates in AtMo) move selected invertZ (Inverts selected z-coordinates in AtMo) move unselected invertX (Inverts unselected x-coordinates in AtMo) move unselected invertY (Inverts unselected y-coordinates in AtMo) move unselected invertZ (Inverts unselected z-coordinates in AtMo) move all invertMove D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 (Moves all coordinates in AtMo such that x_new = D1*x_old + D2*x_old + D3*z_old + D4, y_new = D5*x_old + D6*x_old + D7*z_old + D8, z_new = D9*x_old + D10*x_old + D11*z_old + D12) move selected invertMove D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 (Moves selected coordinates in AtMo such that x_new = D1*x_old + D2*x_old + D3*z_old + D4, y_new = D5*x_old + D6*x_old + D7*z_old + D8, z_new = D9*x_old + D10*x_old + D11*z_old + D12) move unselected invertMove D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 (Moves unselected coordinates in AtMo such that x_new = D1*x_old + D2*x_old + D3*z_old + D4, y_new = D5*x_old + D6*x_old + D7*z_old + D8, z_new = D9*x_old + D10*x_old + D11*z_old + D12) move all invertMove (Moves all coordinates in AtMo such that x_new = D1*x_old + D2*x_old + D3*z_old + D4, y_new = D5*x_old + D6*x_old + D7*z_old + D8, z_new = D9*x_old + D10*x_old + D11*z_old + D12 Double numbers D1-D12 are read from Str var (separated by empty spaces)) move selected invertMove (Moves selected coordinates in AtMo such that x_new = D1*x_old + D2*x_old + D3*z_old + D4, y_new = D5*x_old + D6*x_old + D7*z_old + D8, z_new = D9*x_old + D10*x_old + D11*z_old + D12 Double numbers D1-D12 are read from Str var (separated by empty spaces)) move unselected invertMove (Moves unselected coordinates in AtMo such that x_new = D1*x_old + D2*x_old + D3*z_old + D4, y_new = D5*x_old + D6*x_old + D7*z_old + D8, z_new = D9*x_old + D10*x_old + D11*z_old + D12 Double numbers D1-D12 are read from Str var (separated by empty spaces)) END_COMMAND COMMAND: mv DESCRIPTION: Unix/linux system command for moving file(s). USAGE: Same as unix/linux command. END_COMMAND COMMAND: povray DESCRIPTION: Executes povray from command line. USAGE: povray END_COMMAND COMMAND: print DESCRIPTION: Prints the variable on the screen. USAGE: print (Prints the whole AtomicModel variable) print intensity (Prints the intensity vector in the AtomicModel variable) print pr (Prints the pr vector in the AtomicModel variable) print exp_intensity (Prints the experimental intensity vector in the AtomicModel variable) print exp_pr (Prints the experimental pr vector in the AtomicModel variable) print modeltype (Prints the modeltype of the AtomicModel variable) print comment (Prints the comment line of the AtomicModel variable) print all pdb (Prints the whole AtomicModel variable in pdb-format) print all xyz (Prints the whole AtomicModel variable in xyz-format) print selected pdb (Prints selected atoms in the AtomicModel variable in pdb-format) print selected xyz (Prints selected atoms in the AtomicModel variable in xyz-format) print unselected pdb (Prints unselected atoms in the AtomicModel variable in pdb-format) print unselected xyz (Prints unselected atoms in the AtomicModel variable in xyz-format) print (Prints the whole PdbData variable) print record_name (Prints the given record of the PdbData variable) print RECORDS (Prints all records of the PdbData variable) print MODELS (Prints all models of the PdbData variable) print MODEL int1 (Prints int1 model of the PdbData variable) print (Prints the String variable) print (Prints the StringVector variable) print int1 int2 (Prints the StringVector variable from line int1 to line int2) END_COMMAND COMMAND: pwd DESCRIPTION: Unix/linux system command for printing the working directory path. If String variable is given as argument then working directory is stored to it. USAGE: pwd (Prints current working directory on the screen) pwd (Stores current working directory to String variable) END_COMMAND COMMAND: quit DESCRIPTION: Terminates the program. REMARKS: Outputs the exit text. END_COMMAND COMMAND: rand32 DESCRIPTION: Generates 32-bit random numbers with Mersenne Twister generator. USAGE: rand32 add unsigned_int_seed (Adds new random number generator and initializes it with unsigned_int_seed) rand32 clear (Clears all random number generators) rand32 init gen_index unsigned_int_seed (Initializes random number generator gen_index with unsigned_int_seed) rand32 generate gen_index rand_type (generates one random number with generator gen_index and stores to String variable. SEE REMARKS about rand_types) rand32 generate gen_index rand_type size_int (generates size_int random numbers with generator gen_index and stores them to StringVector variable) rand32 generate_file gen_index rand_type size_int (generates size_int random numbers with generator gen_index and stores them to file given in String variable) REMARKS: rand_types are 0: unsigned long on interval [0,0xffffffff] 1: long on interval [0,0x7fffffff] 2: double on interval [0,1] 3: double on interval [0,1) 4: double on interval (0,1) END_COMMAND COMMAND: rand64 DESCRIPTION: Generates 64-bit random numbers with Mersenne Twister generator. USAGE: rand64 add unsigned_int_seed (Adds new random number generator and initializes it with unsigned_int_seed) rand64 clear (Clears all random number generators) rand64 init gen_index unsigned_int_seed (Initializes random number generator gen_index with unsigned_int_seed) rand64 generate gen_index rand_type (generates one random number with generator gen_index and stores to String variable. SEE REMARKS about rand_types) rand64 generate gen_index rand_type size_int (generates size_int random numbers with generator gen_index and stores them to StringVector variable) rand64 generate_file gen_index rand_type size_int (generates size_int random numbers with generator gen_index and stores them to file given in String variable) REMARKS: rand_types are 0: unsigned long long on interval [0, 2^64-1] 1: long long on interval [0, 2^63-1] 2: double on interval [0,1] 3: double on interval [0,1) 4: double on interval (0,1) END_COMMAND COMMAND: rename DESCRIPTION: Renames variable. If variable name is already in use nothing is done. USAGE: rename old_variable_name new_variable_name (Renames old_variable_name to new_variable_name) END_COMMAND COMMAND: reset DESCRIPTION: Resets input and output controls and clears all variables. USAGE: reset END_COMMAND COMMAND: richtext DESCRIPTION: Provides some simle operations to richtext ctrl. USAGE: richtext edit on (Enables editing to richtext ctrl) richtext edit off (Disables editing to richtext ctrl) richtext load filename (Loads the current content in the richtext control to the file filename. Filename extension is checked automatically. Currently only *.txt format is supported.) richtext save filename (Saves the current content in the richtext control to the file filename. Filename extension is checked automatically. Currently only *.txt format is supported.) END_COMMAND COMMAND: rm DESCRIPTION: Unix/linux system command for removing a file. USAGE: Same as unix/linux command. END_COMMAND COMMAND: rmdir DESCRIPTION: System command for removing a directory. USAGE: Same as unix/linux command. END_COMMAND COMMAND: rotate DESCRIPTION: Performs operations for molecule rotators. USAGE: rotate add (add one molecule rotator) rotate add int1 (add int1 molecule rotators) rotate clear (Erases all molecule rotators) rotate del int1 (Erases molecule rotator int1) rotate generate int1 all (Rotates all coordinates in AtMo var with molecule rotator int1) rotate generate int1 selected (Rotates selected coordinates in AtMo var with molecule rotator int1) rotate generate int1 unselected (Rotates unselected coordinates in AtMo var with molecule rotator int1) rotate generate int1 atom int2 (Rotates atom int2 in AtMo var with molecule rotator int1) rotate generate int1 amino int2 (Rotates amino int2 in AtMo var with molecule rotator int1) rotate generate int1 atoms int2 int3 (Rotates atoms from int2 to int3 in AtMo var with molecule rotator int1) rotate generate int1 aminos int2 int3 (Rotates aminos from int2 to int3 in AtMo var with molecule rotator int1) rotate print (Prints all molecule rotators) rotate print int1 (Prints molecule rotator int1) rotate set int1 id (Set id to String variable for molecule rotator int1) rotate set int1 x1 double1 (Set x1 to double1 for molecule rotator int1) rotate set int1 y1 double1 (Set y1 to double1 for molecule rotator int1) rotate set int1 z1 double1 (Set z1 to double1 for molecule rotator int1) rotate set int1 x2 double1 (Set x2 to double1 for molecule rotator int1) rotate set int1 y2 double1 (Set y2 to double1 for molecule rotator int1) rotate set int1 z2 double1 (Set z2 to double1 for molecule rotator int1) rotate set int1 all double1 double2 double3 double4 double5 double6 double7 (Set all rotator params (x1,y1,z1,x2,y2,z2,alpha) for molecule rotator int1) rotate set int1 vec1_from_str (Set rotate vector 1 (x1,y1,z1) from Str var. x1,y1 and z1 are given in a single string separated by empty spaces) rotate set int1 vec2_from_str (Set rotate vector 2 (x2,y2,z2) from Str var. x2,y2 and z2 are given in a single string separated by empty spaces) rotate set int1 alpha_from_str (Set rotator int1 param alpha from Str var) rotate set int1 all_from_str (Set all rotator parms (x1,y1,z1,x2,y2,z2,alpha) from Str var. All params in the Str var are separated by empty spaces) END_COMMAND COMMAND: save DESCRIPTION: Saves variable(s) to file. USAGE: save file intensity (Saves AtomicModel variable's intensity vector to the dat-file given in the String variable) save file pr (Saves AtomicModel variable's pr vector to the dat-file given in the String variable) save file exp_intensity (Saves AtomicModel variable's exp_intensity vector to the dat-file given in the String variable) save file exp_pr (Saves AtomicModel variable's exp_pr vector to the dat-file given in the String variable) save file pdbfile (Saves AtomicModel variable to the pdb-file given in the String variable) save file pdbfile all (Saves AtomicModel variable to the pdb-file given in the String variable) save file pdbfile selected (Saves AtomicModel variable to the pdb-file given in the String variable) save file xyzfile (Saves AtomicModel variable to the xyz-file given in the String variable) save file xyzfile all (Saves all atoms of the AtomicModel variable to the xyz-file given in the String variable) save file xyzfile selected (Saves selected atoms of the AtomicModel variable to the xyz-file given in the String variable) save file (Saves StringVector variable to the file given in the String variable) save file int1 int2 (Saves StringVector variable (lines int1 to int2) to the file given in the String variable) save file (Saves PdbData variable to the file given in the String variable) save file (Saves AtomicModel variable with PdbData variable headers to the file given in the String variable) save file all (Saves AtomicModel variable with PdbData variable headers to the file given in the String variable) save file selected (Saves AtomicModel variable with PdbData variable headers to the file given in the String variable) save file int1 int2 (Saves PdbData variable models (from int1 to int2) to the file given in the String variable) save var (Saves all variables to the file given in the String variable) save var variable1 ... variableN (Saves variables variable1 ... variableN to the file given in the String variable) END_COMMAND COMMAND: select DESCRIPTION: Selects or unselects atoms in AtomicModel variable. USAGE: select clear (Empties all selections in the AtomicModel variable) select add all (Selects all atoms in the AtomicModel variable) select add backbone (Selects the backbone of the AtomicModel variable) select add amino int1 (Selects amino acid with resSeq int1) select add atom int1 (Selects atom with serial int1) select del amino int1 (Unselects amino acid with resSeq int1) select del atom int1 (Unselects atom with serial int1) select add aminos int1 int2 (Selects amino acids with resSeq from int1 to int2) select add aminos AMINO_NAME1 ... AMINO_NAMEN (Selects amino acids with resNames AMINO_NAME1 ... AMINO_NAMEN) select add atoms int1 int2 (Selects atoms with serial from int1 to int2) select add atoms ATOM_NAME1 ... ATOM_NAMEN (Selects atoms with names ATOM_NAME1 ... ATOM_NAMEN) select del aminos int1 int2 (Unselects amino acids with resSeq from int1 to int2) select del aminos AMINO_NAME1 ... AMINO_NAMEN (Unselects amino acids with resNames AMINO_NAME1 ... AMINO_NAMEN) select del atoms int1 int2 (Unselects atoms with serial from int1 to int2) select del atoms ATOM_NAME1 ... ATOM_NAMEN (Unselects atoms with names ATOM_NAME1 ... ATOM_NAMEN) REMARKS: Select commands with option amino or aminos work only for AtomicModels with modelType = 1 END_COMMAND COMMAND: selected DESCRIPTION: Prints selected atoms(aminos) serials(resSeqs) in the AtomicModel variable. USAGE: selected atom selected amino REMARKS: Selected commands with option amino or aminos work only for AtomicModels with modelType = 1 END_COMMAND COMMAND: set DESCRIPTION: Sets value for the variable. USAGE: set (Sets AtomicModel variable1 to AtomicModel variable2) set comment (Sets AtomicModel variable commentline to String variable) set int1 (Sets AtomicModel variable to model int1 from the file given in the String variable) set int1 (Sets AtomicModel variable to int1 model of PdbData variable) set clear_headers (Clears all header RECORDS from PdbData variable) set (Sets PdbData variable from the file given in the String variable) set RECORD_NAME clear (Clears record RECORD_NAME from the PdbData variable) set RECORD_NAME (Sets PdbData variable record from the StringVector variable) set (Sets PdbData variable1 to PdbData variable2) set (Sets String variable1 to String variable2) set (Sets String variable to StringVector variable by cuttind vector elements by '\n'-characters) set int1 int2 (Sets String variable to StringVector variable2 by cutting vector elements by '\n'-characters. Elements form int1 to int2 are read from StringVector variable) set 'text string' (Sets String variable to text string) set (Sets StringVector variable1 to StringVector variable) set (Sets the StringVector variable from the file given in String variable) set int1 (Sets the int1 line of StringVector variable to String variable) set int1 int2 (Sets StringVector variable reading lines from int1 to int2 from the file given in the StringVector variable) set int1 int2 (Sets StringVector variable1 to lines (from int1 to int2) from StringVector variable2) set int1 int2 int3 int4 (Sets StringVector variable1 lines (from int1 to int2) to StringVector variable2 lines (from int3 to int4)) set RECORD_NAME (Sets StringVector variable to section RECORD_NAME from PdbData variable) END_COMMAND COMMAND: setenv DESCRIPTION: Sets the given environmental variable to given value. USAGE: setenv ENVIRONMENTAL_VARIABLE 'value' (Sets the value of ENVIRONMENTAL_VARIABLE to value given between two '-tokens) setenv ENVIRONMENTAL_VARIABLE (Sets the value of ENVIRONMENTAL_VARIABLE to value given inString variable) END_COMMAND COMMAND: sleep DESCRIPTION: Stops the program execution for int seconds. USAGE: sleep int END_COMMAND COMMAND: str DESCRIPTION: Provides some simple manipulations to String variables. USAGE: str -a arg1 ... argN (Appends concatenated arg1 ... argN to String variableRet. args may be String variables or enclosed by two '-tokens.) str -cmp arg1 (Compares String variable1 to arg1. arg1 may be String variable or enclosed by two '-tokens. The result is stored in String variableRet and is 1: if String variable1 is alphabetically larger than args1. 0: if String variable1 is same as args1. -1: if String variable1 is alphabetically smaller than args1. str -p arg1 ... argN (Prepends concatenated arg1 ... argN to String variableRet. args may be String variables or enclosed by two '-tokens.) str -s arg1 ... argN (Puts concatenated arg1 ... argN to String variableRet. args may be String variables or enclosed by two '-tokens.) str -sub int1 int2 (Gets sub-string from String variableOrg and stores it String variableRet. Sub-string starts at index int1 and has length int2.) str -subword int1 (Gets sub-word int1 from String variableOrg and stores it String variableRet.) END_COMMAND COMMAND: strvec DESCRIPTION: Provides some simple manipulations to StringVector variables. USAGE: strvec -a arg1 ... argN (Appends arguments arg1 ... argN to StringVector variableRet. args may be String or StringVector variables) strvec -cmp (Compares StringVector variable1 to StringVector variable2) The result is stored in String variableRet and is 2: if StringVector variable1 is alphabetically larger than StringVector variable2 and both StringVectors have the same size. 1: if StringVector variable1 has more elements than StringVector variable2 0: if StringVector variable1 is exactly same as StringVector variable2. -1: if StringVector variable1 has less elements than StringVector variable2 -2: if StringVector variable1 is alphabetically smaller than StringVector variable2 and both StringVectors have the same size. strvec -p arg1 ... argN (Prepends arguments arg1 ... argN to StringVector variableRet. args may be String or StringVector variables) strvec -s arg1 ... argN (Puts concatenated arg1 ... argN to StringVector variableRet. args may be String or StringVector variables) strvec -str int1 (Stores element int1 of StringVector variable to String variable) strvec -sub int1 int2 (Gets sub-vector from StringVector variableOrg and stores it StringVector variableRet. Sub-vector starts at element int1 and ends at element int2.) END_COMMAND COMMAND: symmetry DESCRIPTION: Performs symmetry transformations according to given space group. USAGE: symmetry space_group ... (Performs the symmetry transformations to Atmo var1 and stores the transformations to Atmo var2 ... Atmo varN. Correct number of Atmo vars must be given according to given space group. Space group may be given as integer (1-230) or by using X-Plor/CNS notation.) END_COMMAND COMMAND: sysinfo DESCRIPTION: Acquires user, system and floating point number information. USAGE: sysinfo (Prints user, system and floating point number information on the screen) sysinfo (Stores user, system and floating point number information to String variable) sysinfo (Stores user, system and floating point number information to StringVector variable) END_COMMAND COMMAND: thread DESCRIPTION: Runs PDBMANAGER commands in different threads. Currently only command calc is implemented and has the same options as ordinary calc command but command starts with thread thread_priority_int. thread_priority_int is integer (0-100) and decides the priority of the launched thread. COMMAND CAN NOT CURRENTLY RUN UNDER COMMAND commandfile! THIS CAUSES THE PROGRAM TO CRASH! USAGE: thread priority_int calc debyeint all double1 int1 (Calculates debyeint for all atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) thread priority_int calc debyeint selected double1 int1 (Calculates debyeint for selected atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) thread priority_int calc pr all double1 int1 (Calculates p(r)-function for all atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) thread priority_int calc pr selected double1 int1 (Calculates p(r)-function for selected atoms in the AtomicModel variable double1 is maximum value and int1 is number of points in the function) END_COMMAND COMMAND: timer DESCRIPTION: Can be used to time operations. It works on milliseconds accuracy. USAGE: timer get (Gets the time elapsed since the previous reset of the timer and stores it to String variable) timer pause (Pauses the timer) timer resume (Resumes the timer) timer scr (Prints on the screen the time elapsed since the previous reset of the timer) timer start (Starts the timer) END_COMMAND COMMAND: var DESCRIPTION: Prints all the variable names with some additional information on the screen. USAGE: var (Prints names and classes of all variables) var -l (Prints names and classes of all variables with additional information) END_COMMAND COMMAND: version DESCRIPTION: Prints the program version on the screen. END_COMMAND COMMAND: view DESCRIPTION: Starts pdb-file viewer with the command given in the variable VIEWER_COMMAND. USAGE: view open arg1 ... argN (Open viewer program as sub process with arguments arg1 ... argN) view close (Close viewer program session) view cmd arg1 ... argN (Sends arguments arg1 ... argN to external viewer program as arguments) EXAMPLE: view open 2BBM.pdb view cmd rotate x 20 view cmd translate y 5 view close REMARKS: The variable VIEWER_COMMAND is located in the file ENVIRONMENT.txt and can be changed. NOTICE: If VIEWER_COMMAND command is not in your PATH variable you have to specify the whole path for the command (For instance, /usr/X11R6/bin/rasmol) Otherwise, it is sufficient to use the viewer program name (For instance, rasmol). END_COMMAND COMMAND: viewobj DESCRIPTION: USAGE: viewobj (Views the whole AtomicModel variable with command VIEWER_COMMAND if modelType of the Atomicmodel variable is 1 pdb-format is used if modelType of the Atomicmodel variable is 2 xyz-format is used) viewobj all pdb (Views all atoms in the AtomicModel variable) viewobj selected pdb (Views selected atoms in the AtomicModel variable) viewobj all xyz (Views all atoms in the AtomicModel variable) viewobj selected xyz (Views selected atoms in the AtomicModel variable) viewobj (Views the whole PdbData variable) viewobj int1 (Views the model int1 in the PdbData variable) viewobj int1 int2 (Views the models int1 to int2 in the PdbData variable) viewobj all (Views all atoms in the AtomicModel variable with header from the PdbData variable) viewobj selected (Views selected atoms in the AtomicModel variable with header from the PdbData variable) END_COMMAND COMMAND: voronoi DESCRIPTION: Generates voronoi vertexes from given AtomicModel coordinates USAGE: voronoi all (Generates voronoi vertex points from all AtMo var coordinates and stores them to file given in the Str var) voronoi selected (Generates voronoi vertex points from selected AtMo var coordinates and stores them to file given in the Str var) END_COMMAND