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make background s_external cmds [command=s_icmCmdsUponCompletion] [info=s_Message] [name=s_jobName] [simple]This command runs a set of external commands written in a form that can be executed as an external process. Upon execution of these external commands the ICM client willreceive the s_Message ( by default it will be the following message: "background job 'jobName' completed. Press OK to load the results".You can also specify which commands can be executed by the ICM client to loadthe results of this job. Arguments:s_externalCommands # e.g. "grep a *.tx >! b" use Path() function to run an ICM threadname= s_jobName # e.g. name= "j1"command= s_\n_separated_list_of_ICM_commands # default is empty string.info= s_completionMessage # e.g. "Finished. Press OK to read the model" The make background command the following features:it is portable and works under different operating systems.it needs ICM in the GUI mode ( icm -g )to specify a correct external ICM call, you can use the Path( unix, s_options ), e.g. make background Path(unix "_action ") command="read object OUTPUT\nread stack OUTPUT"simple option creates completely detached job. ICM will not keep any information about that process.This option is useful if you want simply to launch an external program and don't want to have any further interaction with it.make background "ls > tmp.txt" command="read string \"tmp.txt\" " info="" # the empty info arg suppressed the dialogshow s_out#make background name="job1" Path(unix,"_myScript","-n","-s") # Path(unix,..) returns current ICM locationA Windows example:make background "\"c:\\Program Files\\Microsoft Office\\WINWORD.EXE\" C:\\Temp\\Doc1.doc" simpleSee also:sys commandUnix functionmake bond: forming a covalent bond make bond as_singleAtom1 as_singleAtom2 [type=i_type] adds a covalent bond between two selected atoms in a non-ICM molecular object (e.g. X-ray or NMR pdb-entries) or resets the bond type (for ICM objects use make bond simpleThe command is used to correct erroneous connectivity guessed by the read pdb command. This correction makes the molecule displayed in the graphics window look better and is necessary before conversion into an ICM molecular library entry (see icm.res or user library files) using the write library command. It can also be useful to display a connected Ca-trace. In interactive graphics mode you may type make bond and then click two atoms with the Control button pressed. The type= option allows one to set the bond type ( i_type =3 , for a single (default), double, triple and aromatic bond, respectively. make bond simple as_singleIcmAtom1 as_singleIcmAtom2 forms a bond, e.g. for peptide cyclization. One needs to unfix the following energy terms forthat bond to be minimized properly:build string "ala ala ala ala ala"make bond simple a_/1/n a_/5/cset term "bb,bs,af"minimize make bonds in an atomic chain make bond chain as_chainOfAtoms connects specified atoms in a linear chain. Useful for PDB entries containing only Ca atoms. Examples: read pdb "4cro" # contains only Ps and Ca's display # Milky sausage make bond chain a_4cro.//p # connect P atoms of the DNA backbone make bond chain a_4cro.//ca # connect Ca atoms of the protein backbone See also: delete bond. make boundary: Poisson electrostaticsa command to prepare for the boundary element electrostatic calculation make boundary [as] this is an auxiliary command which is required if you need to calculate the electrostatic free energy with the boundary element method several times. Optional atom selection as_ from which the electrostatic field is calculated can be specified. This may be the case if the charge distribution changes but the shape does not. However, the boundary does depend on the dielectric constant parameters such as dielConst and dielConstExtern . If you intend to change them the boundary need to be remade every time. This command does not generate any output by itself, it just creates the internal table which can later be used by the show energy command or the Potential( ) function. The dielectric boundary is a smooth analytical surface which is built with the contour-buildup algorithm ( Totrov,Abagyan, 1996 ). The surface looks like the skin surface, but uses different radii which were optimized against experimental LogP data. Both skin and the dielectric boundary uses the same water radius ( the waterRadius parameter). The "electrostatic" radii used by ICM to calculate the boundary are stored in the icm.vwt file. See also: REBEL, surfaceAccuracy, electroMethod, delete boundary, show energy", term "el", Potential( ). Examples: electroMethod="boundary element" read object s_icmhome+"rinsr" delete a_w* # get rid of water molecules make boundary a_1 surfaceAccuracy = 5 # calculate params of the dielectric boundary show energy "el" # electrostatic energy by BEM e1=Energy("el") # extract the energy set charge a_/33/cd*,hd*,ne*,he*,cz,nh*,hh* 0. # uncharge arg33 show energy "el" # electrostatic energy of the uncharged Arg33 e2=Energy("el") # extract the energy print e1-e2 delete boundary # memory cleanup make directory make directory s_Directory make specified directory. Example: make directory "/home/doe/temp/" See also: sys , set directory, delete directory, Path(directory) make disulfide bond make disulfide bond [ only ] as_atomSg1 as_atomSg2 form breakable disulfide bonds between two sets of specified sulfur Sg atoms, regardless of the distance between them. Forming the bond means that two Hg hydrogens of Cys residues are dismissed, a covalent bond between two Sg is declared (but not enforced) and four local distance restraints (see icm.cnt) are imposed. These restraints are indeed local, since two Sg atoms only start feeling each other when they are really close, otherwise the energy contribution is close to zero . Option only causes deletion of previously formed disulfide bonds, otherwise the new one is added to the existing list of disulfide bonds. Examples: build string "se cys ala cys" # sequence containing two cysteins display # display an extended ICM model of the sequence # set only one SS-bond, disregard all previous make disulfide bond a_/1 a_/3 only montecarlo # MC search for plausible conformations See also: delete disulfide bond and (important!) disulfide bond. make drestraint: extract distances structure make drestraint as_select1 as_select2 r_LowerBound r_UpperBound r_LowerCorrection r_UpperCorrection [s_fileNameRoot] create two files containing the list of all the atom pairs specified by two selections (i.e. a_* a_* - all the pairs; a_1//* a_2//* atom pairs between molecules 1 and 2 for which the interatomic distance lies between r_LowerBound and r_UpperBound. Note: it is critical that both selections are in the same object. Only tethers can pull to atoms of a different object. For each pair of atoms a distance restraint type is created with lower bound less than the actual interatomic distance by r_LowerCorrection and upper bound greater than the actual interatomic distance by r_UpperCorrection. This command can be used for example to impose loose distance constraints between two subunits. The number of the formed drestraints is returned in the i_out variable. See also: set drestraint as_1 as_2 i_Type if you want to impose a specific drestraint. Examples: read object s_icmhome+"complex" # load a two molecule complex for refinement # extract all Ca-Ca pairs between 2 and 5 A # for each pair at distance D create distance # restraint type with lower bound D-2.5 and # upper bound D+2.5 make drestraint a_1//ca a_2//ca 2. 5. 2.5 2.5 make factor: FFT calculation of diffraction amplitudes and phases make factor map_Source r_resolution [s_factorTableName[s_ReName[s_ImName]]] calculate structure amplitudes and phases from the given electron density map by the Fast Fourier transformation. The table ' s_factorTableName' with h,k,l and structure factors will be created (further referred to as T for brevity). It will contain the following members: three integer arrays of Miller indices: T.h T.k T.l two rarray of real and imaginary parts of the calculated structure factors. Default names: T.ac and T.bc, respectively. Alternative names can be explicitly provided in the command line. If structure factor table s_factorTableName already exists, structure factor real and imaginary components are created or updated in place. Any other arrays containing experimental, derivative or control information may be added to the table and participate in selections and sorting. Example: read map s_icmhome+"crn" # load "crn.map" set symmetry m_crn 1 make factor 5 5 5 "F" # h_max=k_max=l_max=5 # F.h, F.k, F.l, F.ac, F.bc are created show F group table append F Sqrt(F.ac*F.ac + F.bc*F.bc) "Fc" Atan2(F.bc,F.ac) "Ph" sort F.Fc show F make flat chem_array make flat chem_array [rotate] [hydrogen] [window=r_WidthToHeightRatio] [index=I_indices] [pattern=X_scaffold]convert a chemical array into standard automatically generated 2D chemical drawings in place(compare with Chemical( Smiles( chem_array ), smiles ) which does not touch the source array).A chemical array can created by the read table mol command. The compounds in the source file can be 0D (all coordinates set to 0), 3D or 2D. In all cases these x and y coordinates are can not be used for chemical drawing andone needs to use the above command to generate 2D drawings.The command also preforms rotation for optimal fit into rectangle with specified width to height ratio ( window argument ).Default ratio is 1.5.Other options:rotate : does not coordinate assignment, preforms only best fit rotationhydrogen : keep explicitly drawn hydrogensindex : performs operation only on selected compoundspattern : scaffold with assigned 2D geometry Example: read table mol s_icmhome+"template_3D.sdf" make flat template_3D.molSee also: Chemical , read table mol .make grob map command to contour electron density or grid potentials make grob m_map [header] [solid] [box] [I_indexBox[1:6]] [[exact] [field=]r_sigmar_absValue] [as [margin=r]] [name=s] make grob m_map add r_sigmaIncrement make grob m_map add exact r_absoluteIncrement # build a contour that can be modified make grob g_existingContourGrob add r_sigmaIncrement # rebuilds and redraws an existing contourCreate graphics object by contouring electron density map at a given threshold. threshold: By default the contouring level is calculated as the mean map value (returned by Mean ( m_map ) ) plus mapSigmaLevel times root-mean-square deviation value. If a real value argument is provided, the mapSigmaLevel shell variable is redefined. Option exact allows one to specify absolute value at the contouring is performed. If atom selection is specified, contour will only be built around as_, with the optional additional margin. Helpful in contouring ligand from electron density map.Other options:header this option adds the name of the source map and the command to recalculate the grob at different contour level.Example: build string "his glu" make map potential Box( a_ 3.) make grob m_atoms 3. # 3 sigmas above the mean # make grob m_atoms .2 exact # countour at 0.2 level # .2 or .1 exact is useful to detect almost closed pockets display g_atoms # make grob m_atoms exact 0.15 # at value of 0.15 display g_atoms # mapSigmaLevel = 1.5 make grob m_atoms add 0. # at mapSigmaLevel make grob g_atoms add -0.1 # at 1.4 sigma # loadEDS "1atp" 0. read pdb "1atp" make grob m_1atp 1.5 a_atp cool a_ display g_1atp Defaults: create simple chicken wire map (sections in three sets of planes, NOT solid) take the current map; generate the name of the grob which is the same as the map name except for the g_ prefix; contour the whole map use threshold value from the ICM-shell real variable mapSigmaLevel . mapSigmaLevel is changed if the exact option is used Option solid tells the program to create a solid triangulated surface which can later be displayed by display grob solid command. The threshold is expressed in the units of standard deviations from the mean map value, i.e. 1.0 stands for one sigma over the mean. I_indexBox [1:6] is optional 6-dimensional iarray containing i_startSection i_startRow i_startColumn i_NofSections i_NofRows i_NofColumns . It overrides the default, contouring the whole map. Option box adds surrounding box to the grob. make grob image command to create a vectorized graphics object. make grob image [name=s_grobName] create a vectorized graphics object (grob) from the displayed wire or solid objects. The information about colors will be inherited. Very useful if you want to export wire, ribbon or CPK into another graphics program, since graphics objects can be written in portable Wavefront (.off) format. Further, graphics objects can exist independently on the molecules which may be sometimes convenient. Also, underlying lines and vertices can be revealed. The graphics object created from the displayed solid representations assigns and retains color information as lit in a given projection. These colors can not be changed. Use special make grob skin command to generate a more elaborate graphics object from skin . Examples: read object s_icmhome+"crn" ds a_crn.//!h* ribbon # ribbon make grob image name="g_rib" display g_rib smooth only # try select g_rib and Ctrl-X,Ctrl-E/W etc. # option smooth eliminates the jaggies. write g_rib # save to a file make grob matrix make grob [solid] [bar[box]] [color] M_matrixName [r_istep r_jstep r_kstep] [[name=]s_grobName] Create a three-dimensional plot from M_matrixName, so that x=i* r_istep, y=j* r_jstep and F(x,y)= k* M_matrixName[i,j]. Options: bar : generate rectangular bars for each i,j matrix value instead of a smooth surface. box : add a box around the 3D histogram color : color grob by value according to the PLOT.rainbowStyle preference. solid : tells the program to triangulate the surface Examples: read matrix s_icmhome+"def" make grob def solid display # OR read matrix s_icmhome+"ram" # phi-psi energy surface make grob ram 1. 1. 0.1 # create the surface display g_ram magenta # display it make grob solid ram 1. 1. 0.08 name="g" # create the surface display g solid gold # display it make grob potential make grob potential [solid] [as_1 [as_2]] [[field=]r_potentialLevel] [grid=r_gridCellSize] [margin=r_margin] [[name=]s_contourGrobName]Example:make grob potential a_lig create graphics object of isopotential contours of electrostatic potential which takes not only the point charges but also the dielectric surface charges resulting from polarization of the solvent. This potential need to be calculated in advance by the boundary element algorithm. Contours can be displayed in the wire and solid representations (see also display grob). The default parameters are: r_polentialLevel 0. kcal/mole/electron_charge_units. r_gridCellSize 0.5 A (you may want to increase it up to 2A for speed). r_margin 5.0 A (you may want to reduce it for speed). See also: make map potential, electroMethod, make boundary, show energy "el", term "el", Potential( ). Examples: build string "se his arg glu" electroMethod="boundary element" # REBEL algorithm make boundary make grob potential solid 0.1 grid=2. margin=4. name="g_equipot1" display g_equipot1 transparent blue make grob potential solid field=-0.1 grid=2. margin=4. name="g_equipot2" display g_equipot2 transparent red ds xstick residue label make grob skin or surface make grob skin [wire smooth] [as_1 [as_2]] [[name=]s_grobName] [r_transparency] make grob surface [color] [wire smooth] [as_1 [as_2]] [[name=]s_grobName] [r_transparency] create grob containing the specified molecular surface (referred to as skin). If the wire option is given the transparent wire grob will be created (solid grob is the default). It will have the same default color. The disconnected parts of this grob may later be split . The grob will be named by the default name g_objName unless the name is explicitly specified. The final actual name will be returned in s_out . The smooth option allows one to close the cusps. This closure is necessary to enable the compress grob operation. The compress g_ command allows one to dramatically simplify the triangulated surface and reduce the number of triangles. Typically compress g_ 1. will reduce the number of triangles by an order of magnitude. A grob can later be colored with the color grob potential command. Examples: read object s_icmhome+"crn" # skin around a substructure, (just as an example) make grob skin a_/1:44 a_/1:44 0.6 split g_crn_m display g_crn_m2 a_//* show Area(g_crn_m2), Abs(Volume(g_crn_m2)) make grob skin a_ a_ name="gg1" # display gg1 now make grob skin wire name="gg2" # display gg2 now make grob skin smooth a_/1:20 a_/1:20 name="gg3" compress gg3 1. # simplifies the surface The transparency can also be set with the set grobname r_transparencyLevelcommand.See also: set color to set atom colors Creating 3D label objectsA number of commands in ICM enable the creation of "3D label" objects which help to measure and annotate geometry in the 3D space,like distances and angles. Some 3D labels, like hydriogen bonds, illustrate concepts which depend on the geometry and the structure of molecules.3D labels are stored in a parray object of a "label3d" subtype. 3D labels defined on atoms are dynamic: visual angle/distance information is updated dependingon the changes in the atom geometry.3D label creation commands have similar structure.Commands which are currently available are:make distance to create distance labels;make hbond for hydrogen bonds;make angle for planar angles;make torsion for dihedral angles.Each of these commands has specific arguments. but there i