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set areaatom ballas ..backgroundballbfactorbondcartesianchainchargechiralcolorcommentcomp_matrix conf directorydrestraintediterrorfactorfieldfontforegroundformalformatgrobgroupheaderhydrogen indexkeylabellinkmapmenummffmolcartnameobjectoccupancyplaneproperty .. randomize reflectionresolutionselftetherseparatorsequence reversesiteslidesstructurestackstereostickswisssymmetry tabletautomertermtethertexturetopologytorsiontreetypeview argumentsExample: set bfactor a_//c* 20. set area sequence : positional factors for sequence alignment set area seq [ { R_factors r_factor } ] sets/resets a property array assigned to a sequence. Each amino acid can be assigned a relative solvent accessibility value for this residue in a three-dimensional model. 0. - fully buried (the highest possible factor), 1. - fully exposed. These values can also be used to influence the alignment (buried residues with accessibilities close to zero will have larger contributions). The exact dependence residue-residue score factor on this value is defined by the accFunction array. set area rs [ { R_areas r_area } ] sets/resets an array or accessible area values (or value) to the residue selection. Note that for the residue areas contain absolute values (e.g. 84., 120., etc.) while for sequences (see above) the area/weight values are relative accessibilities in the range [0.,1.]. The maximal possible accessibilities are returned by the Area( rs_ type ) function. Example: read object s_icmhome+\"crn.ob\" show surface area set area a_/asn Area(a_/asn type) # reset areas to maximal values set area a_crn.m 0. set area a_crn.m/ Random(0. 1. Nof(a_crn.m/)) See also: accFunction , Align ( seq1 seq2 area ) set atom label or the ball radius set atom ball as Rsets custom balls to atoms. Can be returned with the Radius( as ) function set atom label as Ssets custom labels to atoms. Can be returned with the Label( as ) functionset atom (re)sets atom properties, such as atom presence ( on and off ) or coordinates set as onoffactivate (unhide) or inactivate (hide) atoms for energy and surface calculations. The inactive atoms can be shown ingraphics as shaded wire models. Example: set a_//h* off ; Nof(a_// off) ; set a_//h* on By default all atoms are active. If a selection of atoms in 'off' or inactive, this state may also be added to the object stack with the store conf atom obj_sel command. Be careful since the very first conf should also be added with the store conf atom .. command for this mechanism to work.See also: Nof( onoff ), set atom ball label , store conf atom .. set as_Natoms M_3xN [mute] set as_Natoms M_3xN [mute]# eg set a_W//vt1 Xyz(a_W//o) set as_tethered_inICMobj [tree] # follows tethers in this case the target coordinates are simply taken from the destination positions for the tethers. set as_one_vt1_atom_inICMobj [R_3xyzM_3x1as] set as_nonICM_X as_ICMtetheredToX # used to update sdf/mol coordinates after optimization. this command is used to inherit the coordinate changes in a converted object with different order of heavy atoms.Imagine the following scenario: a mol file is read into a nonICM object, this object is converted with option tether (the order of heavy atoms may change)the converted object is optimized and the heavy atom coordinates are changednow there is a need to transfer the changed coordinates back to the source atoms in the nonICM object.The latter is achieved via the above set command. set rs s_secondaryStruct # e.g. set a_/1:3 \"HHH\"this command sets phi and psy angles of the selected residues in an ICM object according to the secondary structure set chain ms s_chainSymbolWith a single atom selection, ICM sets a given atom to the center of gravity of the corresponding molecule (no arguments), given point in space ( R_3Dvector argument ) or center of gravity of selected atoms ( as_select argument ). If multiple atoms are selected, ICM sets the specified atoms to their new XYZ positions. The XYZ matrix can be returned by the Xyz (as_) function. If multiple atoms are tethered the coordinates of the tethered atoms can beset to the coordinates of the target atoms (see also minimize tether, superimpose and minimize \"tz\". Examples: build string \"se ala his glu\" set a_/3/ca Matrix(Mean(Xyz(a_//ca))) # 3rd Ca to the center of mass of all Ca s set a_/3/ca Matrix({-3., 12., 14.5}) set a_//vt1 # set the first virtual atom to the center of mass randomize a_//vt1 0.1 # randomize the vt1 position in case of singularity For ICM molecular objects, in the most popular operation (set a_1//vt1) the first of the two virtual atoms (vt1) attached to the beginning of the selected molecule is set to the center of gravity of the same molecule. The purpose of this action is to simplify molecular rotation and translation via the first six free virtual variables. The tvt2 and tvt3 torsions and avt2 planar angle determine rotation of the whole molecule around the axes passing through the center of gravity. Useful for docking. Examples: read object s_icmhome+\"complex.ob\" set a_1//vt1 # now it is easy to rotate the 1st mol. # by changing tvt1 set a_2//vt1 # now it is easy to rotate the second molecule set a_2//vt1 {1. 1. 1.} # move it to {1. 1. 1.} point # # Multiple molecules: let us set vt1 for all water molecules to oxygen # to fix the first 3 variable and keep the oxygen positions unchanged read pdb \"2ins\" convert set a_w*//vt1 Xyz(a_w*//o) fix v_w*//vt1 mc v_w* See also: command description set a_/* s_secondaryStructure to change phi,psi angles according to secondary structure, virtual atoms/variables information about virtual atoms and variables move command which goes further and actually changes the topology of the ICM-tree. set cartesian command that assigns coordinates from a template file set background image in graphics set background image bgimage full set background image bgimage exact center set background image bgimage exact [ origin=I_pos ] [ r_scaleCoeff ]- set image as graphics backgroundWith the exact option the image will be displayed in its own resolution. If center option is provided it will be centered,otherwise you may specify the origin of the left bottom corner with origin option (default {0 0}) and/or scale coefficient.Image created in this mode is drag-able and resize-able by mouse using 'drag-atom' mode.With the full option the image is scaled to the maximum size when it still fits in the window Otherwise the image is scaled so that its central part fully covers the window without margins.Aspect ratio of the image is preserved in all of the above cases. set background image off- clear graphics background (remove any images assigned)Examples: read image s_icmhome+\"splash.png\" set background image album[ Nof(album) ] set bfactor set bfactor as { r_NewFactor R_NewFactors } set bfactor rs R_NewResidueFactors set B-factors of selected atoms to a specified real value (or individual values). To assign individual b-factors, provide a real array with b-factors for each atom. To assign the individual b-factors at the residue level, provide matching residue selection and R_NewResidueFactors array. Examples: build string \"ala his trp\" # also includes N- and C- terminal groups set bfactor a_//* 20. set bfactor a_//ca {20.,10.,30.} # individual atomic factors set bfactor a_/2:18/ca,c,n 10. set bfactor a_/* {10.,20.,30.} # individual residue factors set bond type set bond type as_class1 [ as_class2 ] { i_type } set the bond chemical type (0 - undefined, 1 single, 2 double, 3 triple, 4 aromatic,9 quadruple,10 amid). set bond auto ms with the auto option the command automatically reassigns patterns of single and double bonds. It performs the following operations: identify aromatic rings in object os_ from patterns of single and double bonds. Use preference wireStyle = \"chemistry\" (Ctrl-L) to see the bond types. This is done automatically upon reading of objects, mol and mol2 files if logical l_readMolArom is set to yes. for ICM objects, set ICM bond variable types according to bond chemical type, atom types and distance between them Example: read pdb \"1crn\" display wireStyle=\"chemistry\" set bond type a_//c a_//o 2 # double # standard bonds in a/acids set bond type a_/phe,tyr,trp/[cn][gdez]* a_/arg/cz*,nh* 4 # aromatic set bond type a_/as/cg*,od,od1 a_/gl/cd*,oe,oe1 2 build hydrogen a_/A See also: set bond topology Transfer chemical structure, formal charges and bonds (or atom names), from smiles or a chemical. set bond topology as_ [smileschem1 [label]]The bond orders and formal charges for a molecule in object can be modified according to the smiles string or a chemical if they matchtopologically (i.e. without consideration of bond orders and formal charges). Arguments:as_ atom selection in an ICM or non ICM object, it can also be a selection of different level rs_, ms_ or os_ .smiles string with the new bond orders and formal charges, e.g. \"C1[N+]CCCC1\" for a charged piperedine.chem1 a chemical parray with one chemical in it, it can be read from a mol or sdf file, e.g. read mol table \"myNewChemStruct.sdf\"label : option to transfer atom names from a 2D chemical along with bonds and charges. The atom names can be set in 2D editor with right-click and choosing \"Edit Atom Label\" item. They can be viewed by choosing View/Show full atom names in the View menu. The atom names are stored in the .sdf formatas M ZZC records (e.g. M ZZC 3 cg). The command works as follows:a substructure match without formal charges and bond orders is performed in all molecules and atoms selected (both ICM and non-ICM objects can be treated, but the hydrogens are adjusted only in non-ICM ones)only the 1st match is considered in case of multiple matches of a smiles string or a chemical. The command was meant to fix the whole moleculethe bond orders and formal charges from the first match are transferred to the selection.To apply thie command to an ICM object follow these steps:strip os_ reduce the object to a non-ICM typeset bond topology ms_ s_newSmiles # will fix hydrogens in the changed areasuse convert2Dto3D or 3Dto3D macros if you want to change geometry or do it in the Ligand Editor. set bond topology ms_heteroas_hetero auto guesses bond orders from coordinates (hybridization and angles) but only for molecules of non-ICM type marked as HETATM ( type 'H' ) set cartesian : imposing ring templates set cartesian os [ X_3D_chem_templates ]By default this command is trying to find chemical matches of the selected object witha set of 3D molecules in a template_3D.sdf file ( $ICMHOME directory ) and sets coordinates to the template if a match is found. The file can be modified, or one can use your own external set oftemplates as the X_3D_chem_templates array . Example: read mol s_icmhome+\"template_3D.sdf\" 1 set cartesian a_This command is used in the convert2Dto3D macro.set chain symbol set chain ms_molecules chainSymbolsets the chain character to the selected molecules. Only the first character of thestring is used as the chain identifier. If the chain character is not set is kept as the space symbol (' ') but is shown and can be selected as underscore (_) .Example:read object s_icmhome+\"complex.ob\"set chain a_* \" \" # clean upshow a_C_ # all molecules have blank chain characterset chain a_2 \"A\"set chain a_1 \"B\"show a_CABset charge set charge as_select { r_NewCharge add r_Increment } sets or increments partial electric charges of selected atoms to or by specified real value, respectively. set charge as_select { R_NewChargeArray add R_ArrayOfIncrements } sets or increments partial electric charges of selected atoms to or by a specified real array. The array assignment is useful for saving and restoring the charges. Examples: set charge a_//* 0. set charge a_/lys/nz a_/arg/cz 1.0 set charge a_/asp/od* a_/glu/oe* -0.5 oldCrg=Charge(a_//*) set charge a_//* 0.0 set charge a_/asp/od* a_/glu/oe* add -0.5 # do something with these simplified charges set charge a_//* oldCrg See also: set charge formal, set charge mmff . set charge formal set charge formal as_select r_NewFormalCharge sets formal partial electric charges of selected atoms to or by a specified real value. The charge will be rounded to the nearest value proportional to 1/12th. The following values are common: +-N, +-N/2., +- N/3., +-N/4., +-N/6. Note that the formal charge can not be arbitrarily changed without appropriate changes in the surrounding bond types. The formal charge will be considered by the Smiles function. Example: read object s_icmhome+\"crn.ob\" set charge formal a_//n -0.333 # a formal charge of -1/3. See also: set charge formal auto, set charge, set charge mmff . set charge formal autoassigns formal charges according to pKa base and acids model. set charge formal auto X_chem_arrayms_sel r_pH(7.0)Example:read table mol \"t.sdf\" name=\"t\"set charge formal auto t.mol 7.0 # charge at pH=7Note: this command support nProc option for parallelization.displaying pKa values for chemicals:add column t Chemical({\"CCCCN\",\"CCCNCCC\",\"C(=O)O\",\"CC(=O)O\",\"CCC(=O)O\"}) # we need a chemical table# here is the action on table tadd column t Predict( t.mol \"MolpKaBase\" ) name=\"pkab\"add column t Predict( t.mol \"MolpKaAcid\" ) name=\"pkaa\"set label t.mol t.pkab window= {0.,14.} set label t.mol t.pkaa window= {0.,14.}set format t.mol comment = \"only the lowest number is significant\" set charge mmff set charge mmff as_select set atomic charges according to the rules described in a series of publications on the Merck Molecular Force Field abbreviated as MMFF94 or just MMFF. This command requires the mmff atom types (see the set type mmff command). Do not be surprised that the methyl groups have zero partial charges. That is how they are defined in the MMFF algorithm. This command is automatically executeif you specify option charge in the set type mmff command. Example: read object s_icmhome+\"crn.ob\" set type mmff # mmff atom types show atom type mmff set charge mmff # charges # read mol s_icmhome+\"ex_mol.mol\" for i=2,Nof( object ) set object a_$i. display build hydrogen convert set charge mmff display ball color a_//* Charge(a_//*)//{-1., 1.} ball endfor See also: set charge, set charge mmff . set chiral set chiral as [ 0123 ]set a chiral flag for the selected atoms. The meaning of the flag:0 chirality is not set1 R-chirality2 S-chirality3 a racemic mixture of two chiral isomersIf no explicit integer flag is specifiedthe program will automatically assign the flag from the local geometry and topology.set chiral chemical set chiral chemarray [offinverse]off : converts all chiral centers to racemicinverse : inverts chirality set color directly and without graphics set color site [color] seq1 seq2 .. set color atom_representation_or_label as color set color ribbonbase{residue label} rs colorAllowed atom representations:wirestickballxstickcpkskinsurfacesiteatom labelvariable labelThe set color command is equivalent in action to the color full command (e.g. color a_*. full alignment ). Option full allows one to set colors regardless of the display status.Coloring sequence alignments set color alignment [{i_color_Schema_Nums_color_SchemaName}]Sets alignment coloring schema. If no schema number is provided then default will be set.To modify existing color schemes or introduces new ones you have three different options:modify the content of the CONSENSUSCOLOR.tabfilecolor alignment dynamically by the set color alig R s_rainbow commandset a named numeric field to each position in the alignment with the set field alig s_field i_fieldNumber (1,2,3) R and choose the field from the Color combo. set color alignment R_values [s_rainbow] The R_aliPosValues can be calculated set for each position of the alignment or assigned from sequences via the Rarray( R_prop ali seq ) projection function.Note that s_rainbow will redefine the GRAPHICS.alignmentRainbow variable.Optionally, you can provide minimum and maximum values as an extra two elements of the array: Trim(R, a,b)//a//bExample:read binary alignment s_icmhome+ \"example_alignment.icb\"set color alig \"icm-combo\"set color alig # default 'consensus-strength' will be setset color alig Rarray(Count(Length(alig))) # by default rainbowset color alig Rarray(200,1.)//Rarray(176,2.) \"pink/white/yellow/lightblue\"Setting color by user-defined field. set field alig s_field_name i_fieldNumber (123) R_colors these colors are controlled by the GRAPHICS.alignmentRainbow strings_color_SchemaName can also be a name of the field set in set field commandExample:read binary alignment s_icmhome+ \"example_alignment.icb\"GRAPHICS.alignmentRainbow = \"pink/white/lightblue/yellowgreen\"set field alig 1 \"random_colors\" Random(0., 1., Length(alig) ) # 1st user fieldset color alig \"random_colors\" # or select Color from GUISee also: color , GRAPHICS.alignmentRainbow , set comment set comment [ append ] os_Object s_comment set comment msrs s_comment set a text comment string (or a long name) to object, molecule(s) or residue(s). This annotation is preserved in the read object and write object commands. Examples: read object s_icmhome+\"crn.ob\" set comment append a_ \"\\n The template for modeling\\n Energy minimized\\n\" build smiles \"CCO\" set comment a_1 \"ethanol\" set comment conf [os] s_comment i_confsets a comment string to the stack's conformation.Example:build string \"ASD\"store conf a_set comment conf a_ 1 \"initial conf\" See also: Name conf store conf See also: set comment s_alterSymbol as , Namex function set a flag of an alternative atom position set comment s_charAlterSymbol as_alterAtoms set alternative status to the selected atoms (e.g. set comment a_//Aa \" \" ,to clear the alternative flag). The alternative flag can be read from a pdb file. This flag marks alternative geometrical positions of atoms which are described in the previous ATOM records. For example, the same side-chain or a water molecule can occupy several positions. The symbol of alternative position (usually 'a','b' or 'c' character, since ICM converts the strings to low case) precedes the residue name field. The alternative positions can also be selected with the a_//A alterChar selection. Example: read pdb \"1cbn\" # has alternative positions show a_//Ab # show alternative pos. 'b' set comment a_//Aa \"x\" # rename 'a' positions to 'x' # # example in which we delete all secondary alternatives and # clear the alternative-flag from the main alternative # read pdb \"1hyt\" set comment a_//Aa \" \" # cleared the main alternative delete a_//A # delete atoms with any alter-symbols, eg b,c,2,3 etc. set comment to a sequence set comment [ append ] seq s_comment set comment to a sequence. This sequence comment can be extracted with the Namex( seq )command. Example: a=Sequence(\"AFSGDHAGSFDSGAHGSDFASGDA\") set comment a \"a random test sequence\" See also: SEQUENCE.restoreOrigNames set comp_matrix: redefine residue comparison matrix. set comp_matrix [ add ] r_increment [ s_ijPattern ] change the numbers in the residue comparison matrix, called comp_matrix by a number typically between 0. and 0.2. This may be very important for generating a reasonable alignment for sequences with low sequence similarity. The result is similar to reducing the gapOpen parameter by about 0.1. Examples: set comp_matrix add 0.05 # try to Align( ) again set comp_matrix 10. \"CC\" # make C-C alignment really important set comp_matrix add 1. \"[KR][KR]\" # downweight alignment of Gly against # all the residues set comp_matrix add -.4 \"G\" set comp_matrix 0. \"[AGS][AGSLI]\" set directory set directory s_newDirectory change the current working directory from inside the icm-shell. We recommend using: alias cd set directory \"$1\" . In this case you can change directory in the Unix/DOS style. Example: make directory \"/usr/tmp\" # create a new directory set directory \"/usr/tmp\" cd .. # uses alias from _aliases. # cd .. is equivalent to set directory \"..\" show Path(directory) See also: make directory, delete directory, Path(directory) set drestraint Set a distance restraint between two atoms, or two equal size array of atoms set drestraint as_atom1 as_atom2 i_DrestraintType R3_low_upper_weight Set a distance restraint from interatomic distances set drestraint distpairs [os_ICM] [i_cntype] [only] [find [edit]] [l_info=no]Distances (connections) between two atoms (see distance) can be established from the interface or make distance command pairs of atoms can be created with a make distance command. The convenience of this command is that this object can be easily created interactively and drestraints can be directly created based on the atom pairs of this distance-object. Prerequisites:an ICM object for distance restraints (note that drestraints could only be implsed between atomsof the same ICM object)a distance object ( you can find it in the ICM with the list parray command, usually the collection of distances is called distpairs )the distances do not need to be between the atoms of the target ICM object. It is sufficient that the atoms mentioned in the distpairs object have the same cartesian coordinates as the target atoms (see the find option). Arguments and Options:Argument Default Definition or Commentdistpairs none a set of atom pairs, the current distances are not used, just the atomsos_ICM current object of ICM type this object must contain i_cntype commands finds a type for a close contact between the two atoms drestraint type defining its parameters. Use show drestraint type to see the predefined types, set a new type if necessary.R3_lw_up_wt sets simple typeless harmonic drestraints Alternative to the i_cntype . Example: 0.//0.//1. or 0.//3.//10. only delete all drestraints that previously existed in the objectfind [edit] finds atoms in the specified target object or current object with the same coordinates as the distpairs atoms. With the edit option ICM requires the source atoms to be between ligand and receptor.l_info=no current value in the shell to suppress the output, you may also use l_warn=no to suppress warnings ActionIdentifies atoms in the distance object, finds the same atoms in the os_ICM ( option find ) oruses only atom pairs in a_*.LIG molecule and a_REC. object and sets a distance restraint between them.If the type is not specified with the i_cntype parameters, the type is found automatically achieve a van der Waals contact between two atoms in question. Outputthe drestraintsi_out returns the number of restraints imposedOption all . Set a distance restraint between two groups of atoms ( NMR ) set drestraint all as_atomGroup1 as_atomGroup2 i_DrestraintType sets distance restraints of specified type between selected sets. Drestraint types (integer numbers) can be either read from a *.cnt type file or set directly by the set drestraint type command and shown by the show drestraint type command. Setting NMR-style group restraints and with R-6 averaging.Suppose that you have an NMR restraint (with weight 10., and bounds 3. and 4. ) between hydrogens belonging to a group, e.g. hb1,hb2 or hb3 of alanine2 and ha1 or ha2 of a glycine10. In this case you can use these commands:read object s_icmhome+\"crn.ob\"set drestraint type 1 10. 3. 4.set drestraint all a_/2/hb* a_/10/ha* 1 # type 1 # Info> one multicenter (3x2) dist. restraint imposedshow energy \"cn\" # gives you the penalty valueset terms \"cn\"minimize # minimizes the multi-center restraintOption all allows you to generate a multicenter restraint. Later, the penalty of this restraint will be calculated by finding an averaging the inverse six powersof all possible cross-distances between the two groups.Two methods for averaging are available, see the cnMethodAverage preference. Important: Drestraints can only be imposed on real atoms, the virtual atoms such as vt1,--vt2 are ignored in the cn calculation, therefore the set drestraint a_1//vt1 a_2//vt2 5 command is INCORRECT. Examples: set drestraint a_/15/ca a_/18/ca 5 # distance restraint of type 5 set drestraint type 2. 4. 5.; set drestraint i_2out a_/15/ca a_/18/ca # define new type (i_2out) and set it set drestraint type set drestraint type [ i_DrestraintTypeNumber ] r_WeightingFactor r_LowerBound r_UpperBound [ local r_Sharpness ] creates a distance restraints type. Drestraint types (integer numbers) can also be read from a *.cnt type file and command and shown by the show drestraint type command. If the type number is not specified, it is set automatically and returned in i_2out . Examples: # type 11, weight 10., bounds [1.,3.]A set drestraint type 11 10. 1. 3. # local type, sharpness 5. set drestraint type 12 10. 1. 3. local 5. # automated type set drestraint type 10. 1. 3. local 5. # returns in i_2out set drestraint i_2out a_/2/ca a_/4/ca set group column set group column tableColumn [off]this command is applied to a sorted column in a table changes the view of a table. All the rows with identical cell values for this column are merged intofamilies and the right arrow click is enabled to rotate over thethe family members. Use option off to disable this mode.Example:group table t {1 2 2 3 3 3} {1.1 2.2 3.3 4.4 5.5 6.6}set group column t.A # watch the result in GUI, use arrowsset hydrogen : re-calculating coordinates of hydrogens from the connected heavy atoms set hydrogen [as]This command does not create hydrogens, it takes the existing hydrogens and re-calculates theircartesian coordinates from the corresponding heavy atoms. Warnings: the hydrogen placement by this command is not optimized (see minimize cartesian ). The previously optimized positions of hydrogens may be moved to sub-optimal positions by this command. This command is best used to create reasonable initial positions for hydrogensafter the heavy atom coordinates are re-set.See also: set atom , build hydrogen .set site set site [ only ] seq I_positions s_siteString [type=\"SITE\"] set site [ only ] seq s_swissprotSiteString set-site [ only ] {msseq} [seq_from [ali]] set-site [ only ] ms swiss # find a_P uniprot parent sequences and use them set site [ only ] [display] rs s_siteString [label=0-4] [type=\"SITE\"] set site distance ms [ r_siteArrowLength (0.) ] set site ali column=I_pos color=I_rgb type=\"REGION\" comment=s_text set site to with the specified positions and comment. The default action is append . Option only erases all site information before setting a new one. If the string is specified, create a new site according to the provided legal site string s_siteString (e.g. \"FT ACT_SITE 15 15 Catalytic residue\"). The format of the site string is the same as in the swissprot sequence entries. The list of legal site types is given in the Glossary. The site residues in objects can be delete with the delete site command and selected with the a_/F SiteCodes selection, (e.g. a_/FAB selects residues involved in binging and active site). Option label= sets local SITE.labelStyle . Value 0 means 'unset'.The distance option allows one to set the length of the site arrow. The default is zero.Caution: the set site distance command will re-set all site arrow lengths in a current molecule.Example: read sequence s_icmhome+\"s.seq\" set site sss \"FT ACT_SITE 15 15 active site residue\" set site sss {10,15,16,17} \"Site1: active site\" # the residues of this site can be selected as a_/F\"Site1*\" # read pdb \"2abx\" readUniprot \"NXL1A_BUNMU\" set a_a swiss \"NXL1A_BUNMU\" set site a_P swiss See also: copy site, delete site, showsite{show site} and color site. set site alignment set site ali {icol(1) [,jseq(1), [,ncol(1),[nseq]]]} [column[=I_cols]] [comment=s] [type='SHADE''BOX''FNT''FNT_BLD''REGION'] [color=..] set site ali column=I_pos color=I_rgb type=\"REGION\"\"REGION_VERTICAL\" comment=s_text set site ali column=I_2pos color=I_rgb type=\"DISULFIDE\" comment=s_textannotates a region in the alignment. Example: set site alig column={4,5,6,7,8} type=\"REGION\" comment=\"text\" # sets upper region annotation for columns 4-8 set site alig {10,2,5,5} type=\"BOX\" color=red # draw the box at row=2, col=10 size=5x5 border color red# more elaborate labels of different size marks={'Circle','DTriangle','Diamond','Cross','DiagCross','UTriangle','LTriangle','RTriangle','Pentagon','Hexagon'} marks_siz = marks + \"_\"+ (Count(marks)*5 + 20) set site alig column=Count(10) type=\"REGION_VERTICAL\" color={0,120,230} comment=marks_sizExample (annotate binding sites) read binary s_icmhome + \"example_alignment.icb\" set site alig column=Index( alig, Sphere( a_H [1] a_A 4. ) ) type=\"BOX\" color=redSee also: delete site alignment copy site copy site [ only ] { seq_to ms_to } seq_from [ ali ] transfer (or reassign) sites from a sequence or string to a destination sequence seq_to or a selection of molecules ms_to . Sites are listed in feature tables of swissprot entries and are read by the read sequence swiss command. If alignment is not provided, the sequences will be automatically aligned to find residue-residue correspondences and the reliability of the alignment will be reported. If the source of sites is not provided the sites will be transferred from the sequences linked to objects. The list of sites and their one-letter codes is given below. Normally this command appends to the list of existing sites, unless the only option is given in which case the old sites are dismissed. The effort is made to avoid repetition and retain only the unique set of sites. Identical site will not be added, e.g. simply repeating the same copy site commandwill not duplicate the number of sites. Example: readUniprot \"PIM1_HUMAN\" read pdb \"1xws\" make sequence a_1.1 a=Align(PIM1_HUMAN,1xws_a) copy site PIM1_HUMAN 1xws_a Info> 8 sites (i_out) appended to 1xws_a copy site PIM1_HUMAN 1xws_a # repeat Info> 0 sites (i_out) appended to 1xws_a See also:siteset siteshow siteSITE.appendStyle ( \"none\" or \"merge source\" ) set site to a residue selection set site [ only ] rs s_sideString assign sites to a molecular 3D object (simpler than the previous Swissprot-like definition). Example: read object s_icmhome+ \"crn.ob\" set site a_/10:13 \"candidates for mutagenesis\" set slide set slide name slideArray s_oldname s_newnameRename object names referenced in a slide array. Useful when an object is renamed after making a slide.Examplenice \"1crn\"add sliderename a_1crn. \"crambin\"display slide index=1set slide name slideshow.slides \"1crn\" \"crambin\"display slide index=1See also: slide set tautomer set tautomer ms i_tau set tautomer rs_his i_tau_1_or_2 \"hid\" \"hie\" \"hip\"switches between different tautomers of small molecules ms or histidine rs_his by relative tautomer number or histidine tautomer name.The states and necessary hydrogens are built/set by the build tautomer command.Example: build string \"AHW\"build tautomer a_/his # adds a hydrogen and hydrogen masks to allow the switchingset tautomer a_/his 2See also: build tautomerset texture set texture grob imageArrayupdates textures used in the grob. Textures should be in the order provided by the Image command.Common usage would be: get textures, modify them in ICM, and assign them back to grob.See also: ImageExample:read grob \"g.obj\"I = Image( g texture )I = Image( I 256 256 ) # rescale all imagesset texture g I # update images used for texturesset error set errorsets the icm-shell error flag. The flag is returned (and cleared) with the Error() function.Example:if Nof(Getarg(name))==0 set errora=Getarg(\"t\",2)if Error() then print \"Help\"endifset field by number or nameEach object, molecule, residue or atom have a place to store numbers. This place is called a field and has a reference number.In addition, atoms have named fields that can store numbers or text. Also, user fields can be stored in sequence alignments (see the last section of this page)Setting a named field in molecular objects set field name= s_fieldName asrsmsos { ris_FieldValue RIS_arrayOfValues } See the description below , as well as the Field and Select functions.Setting field in molecular objects by number set field asrsmsos { r_FieldValue R_arrayOfValues } [ number= i_fieldNumber ] set field clear asrsmsos [ number= i_fieldNumber ] set user-defined values to atoms, residues, molecules or objects selected. Atoms have one user-field, residues have three, molecules and objects have sixteen. To specify which field you need to set, use the number= option. To extract the property use Field ( selection, i_fieldNumber ) function. Level Max.Nof_fields example Atom 1 set field a_//c* Mass(a_//c*) Residue 3 set field a_/trp 1. number=2 Molecule 16 set field a_W Random(1.,10.,Nof(a_W)) number=12 Object 16 set field a_*. Rarray(Count(Nof(a_*.))) User defined fields can further be 2D or 3D averaged with the Smooth function and selected by with the Select function. Setting a user field in an alignment set field ali i_vectorNumber (1 or 2) [R_aliPosValues] [s_name] Stores rarray of values for each position of the alignment into a user field i_vectorNumber (allowed values are 1 or 2). Each alignment has 2 reserved vectors thatmay be used for different purposes (e.g. a plot on top of the alignment). See also: set color alig_n R_n # to set custom colorsset atomic field from a map set field map [as] [name=s_field_name]sets the interpolated value from a map to an atom according to the coordinates of its center.Example:loadEDS \"3pah\" 0. # loads m_3pah crystallographic 2Fo-Fc map for epinephrineread pdb \"3pah\"set field m_3pah set field a_// name=\"eds\" Field(a_//)display set label atom a_// Sarray(Iarray(100.*Field(a_//)))display ball Select(a_// \"eds 59ce067264