UCSF Chimera Quick Reference Guide labelopt control the information in atom labels scolor color surfaces by volume data or geometry lighting adjust lighting and shininess section move global clipping planes in parallel November 2014 linewidth control the width of wire bonds segment act on segmentation models Commands (*reverse function ˜command available) longbond* show/hide pseudobonds representing missing segments select* select atoms, (de)activate models for motion mask extract volume data bounded by surfaces set* set visual effects, individual model rotation 2dlabels create labels with text, symbols, and arrows in 2D match perform least-squares fitting of specified atoms setattr* set an attribute to a specified value ac enable accelerators (keyboard shortcuts) matchmaker (mmaker)align models in sequence, then in 3D shape create a surface of a specified geometric shape addaa add an amino acid to a peptide N- or C-terminus matrixcopy apply the transformation of one model to another show* display specified atoms, undisplay the others addcharge assign partial charges to atoms matrixget write the current transformation matrices to a file sleep pause script execution for a specified time addh add hydrogens matrixset read and apply transformation matrices from a file solvate add solvent using AmberTools adjust change bond angle or bond length mclip* control per-model clipping sop adjust capping, edit surface models alias* create an alias or list the existing aliases mcopy copysettings from one molecule model to another split partition a molecule model into separate submodels align align twoatoms or sets of atoms along the line of sight measure perform calculations on structures, surfaces, maps start start Chimera tools by name angle measure angles formed by atoms or by axes and planes meshmol create a "molecule" to showsurface mesh as sticks stereo* switch amongst stereo options and mono viewing aniso* showthermal ellipsoids minimize energy-minimize structures stop exit from Chimera aromatic* showring aromaticity modelcolor set color at the model level surface* calculate and display molecular surfaces background set background color,gradient, or image modeldisplay* set display at the model level surfcat (msms cat)group atoms for surface calculations bond* add/delete bonds molmap create a density map from atomic coordinates surfrepr (msms repr)control surface style (solid, mesh, dot) bondzone* makezoning tools use points along bonds morph morph (interpolate) between different structures swapaa mutate amino acids or swap rotamers cd change the working directory move translate models swapna mutate nucleic acid residues center center the viewonspecified atoms movie capture image frames and assemble them into a movie sym* generate symmetry-related copies of a structure changechains reassign chain identifiers msc* color multiscale surfaces to match atoms system send a command to the system shell chirality report the R/S configuration of a chiral center namesel* save and name the current selection thickness move global clipping planes in opposite directions clip* move global clipping planes nucleotides* create special nucleotide representations tile* arrange models in a plane close close a model objdisplay* display graphical objects topography plot values in a volume data plane as surface heights cofr* report or change the center of rotation open* read local files or fetch by ID transparency* makeatoms/bonds, ribbons, and surfaces transparent color* color atoms/bonds, ribbons, labels, surfaces pause pause script execution until the user presses a key turn rotate models colordef define a newcolor perframe* specify commands to be executed at each display frame vdw* display van der Waals (VDW) dot surface combine combine molecule models into a single model play script various complexmotions vdwdefine* set VDWradii coordset play through frames of a trajectory preset apply a predefined combination of display settings vdwdensity set VDWsurface dot density copy save image files rainbow color residues, chains, or models overarange version showcopyright information and Chimera version coulombic color surfaces by Coulombic electrostatics ramachandran showRamachandran plot of protein residues viewdock start ViewDock and load docking results crystalcontacts identify clashes between PDB symmetry copies rangecolor color overarange according to attribute values volume display volume data such as electron density defattr assign attribute values to atoms, residues, or models read execute a command file, updating display at the end vop edit volume data define* calculate and display axes, planes, centroids represent control atom/bond style (wire, stick, bs, sphere) vseries display,process, and save volume series delete delete atoms and bonds reset restore default or savedorientations wait suspend command processing until motion has stopped display* display specified atoms resrenumber reassign residue numbers window adjust the viewtocontain the specified atoms distance* measure distances between atoms, axes, planes, centroids ribbackbone* allowdisplay of both ribbon and backbone atoms windoworigin set graphics windowlocation echo send text to the status line and Reply Log ribbon* display ribbon windowsize* adjust the dimensions of the graphics window export save the graphical scene ribclass set ribbon residue class write save atomic coordinates (pdb, mol2) fillring* showrings as filled ribinsidecolor* set a separate color for inside protein helix ribbons writesel write a list of the currently selected (or unselected) items findclash* identify clashes and contacts ribrepr control ribbon style (flat, edged, rounded) zonesel select atoms/surfs within cutoffofspecified atoms/surfs findhbond* (hbonds)identify hydrogen bonds ribscale control ribbon scaling (Chimera default, licorice) Miscellaneous Operations (Default Settings) fitmap fit atoms or map into map ribspline control ribbon path (B-spline or cardinal spline) fly smoothly traverse a series of savedpositions rlabel* display residue labels selection from screen Ctrl-left mouse button focus* adjust the viewand center of rotation rmsd evaluate the RMSD between specified sets of atoms add/toggle selection Shift-Ctrl-left mouse button freeze stop all motion rock rock (rotate back and forth) rotation left mouse button getcrd report coordinates roll roll (rotate continuously) XY-translation middle mouse button help display the manual page for a command rotation* makeabond rotatable scaling right mouse button or Side View hkcage create icosahedron as hexagon/pentagon mesh runscript run Python script with command-line arguments preferences Favorites... Preferences... intersurf generate and display interface surfaces save save the current Chimera session searching help Help... Search Documentation... invert swap substituents of an atom savepos* save model positions reporting a problem Help... Report a Bug... ksdssp determine secondary structure from protein coordinates scale* scale the view mailing list [email protected] label* display atom labels scene* save/restore scenes (positions, styles, colors, labels, etc.) Copyright © 2014 The Regents of the University of California, All Rights Reserved Specification Symbols @/element=atno atomic # or element symbol Specification Examples Symbol Function Usage @/idatmType=type Chimera atom type # # model number # model (integer) @/label whether the atom is labeled -all models #. submodel number #. submodel (integer) @/label=label text of the atom label #0 -model 0 : residue : residue (name or number) @/labelColor=labcolor color of the atom label #3:45-83,90-98 :: residue name :: residue @/name=name atom name -residues 45-83 and 90-98 in model 3 :. chain ID :. chain @/occupancy=occupancy crystallographic occupancy :lys,arg @ atom name @atom @/radius=radius current VDWradius -lysine and arginine residues :12,14@ca @. alternate location ID @. alt_loc @/serialNumber=n serial number in the input file -alpha-carbons in residues 12 and 14 − range specifies a range of models, @/surfaceCategory=category surface calculation category :12:14@ca submodels, or residues (main, ligand, etc.) -all atoms in residue 12 and the alpha-carbon in residue 14 , name separator separates models or residues, @/surfaceDisplay per-atom surface display bit (can :.A@n,ca,c,o ranges of models or residues, or be true for buried atoms without -atoms named N, CA, C, and O in chain A names of atoms surface) :50.B,.D * whole wildcard matches whole atom or residue -residue 50 in chain B and all residues in chain D names, e.g.,:*@CA specifies the :12-15,26-28.a,45.b Selected Residue Attributes alpha-carbons of all residues -residues 12-15 in all chains (except het/water), 26-28 in chain A, and 45 in chain B = partial wildcard matches partial atom or residue Usage Description names, e.g., @C= specifies all :/areaSAS=sasa solvent-accessible surface area #0.1-3,5 -submodels 1-3 of model 0 and all of model 5 atoms with names beginning with :/areaSES=sesa solvent-excluded surface area C #0.1-3,.5 :/isHet residues in PDB HETATM -submodels 1-3 of model 0 and submodel 5 of all models ? single-char wildcard used for atom and residue names records (or the mmCIF ligand only, e.g., :G?? selects all equivalent) residues with three-letter names -any/all residues automatically classified as ligand beginning with G :/isHelix amino acid residues in helices :.A & protein ; command separator separates multiple commands on :/isStrand or :/isSheet amino acid residues in strands -chain A residues classified as protein :26-28.a,33.a & side chain/base.with CA/C1’ asingle line :/kdHydrophobicity=value Kyte-Doolittle amino acid -or- hydrophobicity z< zone specifier z
Chimera Quick Reference Guide
