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Action XY-rotation selection Z-rotation adding XY-translation Z-translation Preferences searching scaling
autocolor independent bg_color dc_color windowsize wait window writesel x3dsave write texture viewdock tcolor vdw* thickness turn version vdwde®ne* vdwdensity end mesh, another 3D the movie ®le (wire, a to in atoms ®le at continually a a Windows) ®les atoms of (solid, rounded) into shell to viewing then licorice) values on range from bonds model sets others a display display atoms them (not calculations and ) mono one the edged, stack the the system over backbone command default, matrices of surfaces attribute shell and sequence, matrices the select axis (¯at, speci®ed image value to and atoms parallel representation in surface to Z or picture Options selection assemble cpk) of in session models axis matrix or transparency axis updating updating execute undisplay for level ®le orientations system or the Z options or name Z (Chimera level and Y, ribbon molecular surface ®le, ®le, or between models on or residues the motion by speci®ed data, residues current X, stick/tube planes according PDB Y atoms a objects structures saved to model atoms, surface transformation Y, source processing both sphere Chimera orientations stereo for Set/Unset labels to transformation the model the acid and chains, or X, representation scaling frames align acid tools of X, the display rotatable ) control RMSD range images the b+s, group (see representation ) at the color a color the save ) command command transformation clipping Chimera and current view at apply along the or current current models shadowed a a annotated pop image graphical ribbon residue speci®ed bond the ribbon ribbon amino nucleic default amongst repr cat command molecular a attribute command the display the and a bs over the residues, the or an a about the the Chimera and structures from about color display ribbon options an surface matchmaker msms msms apply color write create execute color read name set control display push energy-minimize ( set translate capture send stick, read restore display set allow make control control roll evaluate rock display save save execute move display scale set pause activate start set switch dot) adjust ( mutate mutate send exit calculate set (
matrixcopy rangecolor matrixget neon read rainbow matrixset namesel modelcolor represent objdisplay* push,pop minimize mmaker modeldisplay* move movie pdbrun open* reset ribbon* ribcolor* ribbackbone* rotation ribrepr ribscale roll rmsd rock rlabel* save savepos* source section show* scale* set* sleep select* start setattr* stereo surftransparency* surfrepr swapaa swapna system stop surface* surfcolor surfcat
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control create add/delete control make make enable measure add assign color change report add create align chain center control create display move close report control save determine restore color de®ne display measure delete adjust assign send generate superimpose show/hide stop report ( display identify
bondrepr 2dlabels bond* bonddisplay brotation bondzone* ac angle addaa addcharge bondcolor* cd chirality addh alias* align chain center labelopt conic label* clip* close cofr* linewidth copy ksdssp load color* colordef display* distance* delete focus defattr echo intersurf match longbond* freeze getcrd hbonds* help ®ndclash* Atom Speci®cation Symbols @/defaultRadius=rad rad is the default VDW radius #/lineWidth=width width is the wireframe linewidth Symbol Function Usage @/display whether display is enabled at the #/pointSize=size size is the dot size in VDW surfaces ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ atom level # model number # model (integer) #/vdwDensity=density density is the dot density used for VDW @/element=atno atno is the atomic number surfaces
#. submodel number #. submodel (integer) ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ : residue : residue (name or number) @/idatmType=type type is the atom type :: residue name :: residue @/label whether the atom is labeled Atom Speci®cation Examples #0 @/label=label label is the text of the atom label :. chain ID :. chain - all atoms in model 0 @ atom name @atom @/labelColor=labcolor labcolor is the color of the atom #3:45-83,90-98 label @. alternate location ID @. alt_loc - residues 45-83 and 90-98 in model 3 @/name=name name is the atom name :lys,arg − range speci®es a range of models, - lysine and arginine residues submodels, or residues @/occupancy=occupancy occupancy is the occupancy :12,14@ca , name separator separates models or residues, @/radius=radius radius is the current radius (may - alpha carbons in residues 12 and 14 ranges of models or residues, or have been changed from the :12:14@ca names of atoms default VDW radius) - all atoms in residue 12 and the alpha carbon in residue 14 * whole wildcard matches whole atom or residue @/serialNumber=n n is the atom serial number in the :.A@ca,c,n,o names, e.g.,:*@CA speci®es the input ®le - peptide backbone atoms in chain A alpha carbons of all residues @/surfaceCategory=catname catname is the category the atom :50.B,.D = partial wildcard matches partial atom or residue belongs to for surface calculation - residue 50 in chain B and all residues in chain D names, e.g., @C= speci®es all purposes (main, ligand, etc.) :12-15,26-28.a,45.b atoms with names beginning with @/surfaceColor=surfcolor surfcolor is the color of the - residues 12-15 in all chains (except het/water), 26-28 in chain A, C atom's molecular surface and 45 in chain B ? single-char wildcard used for atom and residue names @/surfaceDisplay whether molecular surface #0.1-3,5 only, e.g., :G?? selects all display is turned on for the atom - submodels 1-3 of model 0 and all of model 5 residues with three-letter names #0.1-3,.5 beginning with G @/vdw whether VDW surface display is - submodels 1-3 of model 0 and submodel 5 of all models turned on for the atom ; command¢ ¢ ¢ ¢ ¢ separator¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ separates¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ multiple¢ ¢ ¢ ¢ ¢ ¢ ¢ commands¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ on¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ligand a single line - any/all residues automatically classi®ed as ligand z< zone speci®er z
@/altLoc=¢ ¢ ¢ ¢ ¢ ¢ altloc¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ altloc¢ ¢ ¢ ¢ ¢ is¢ ¢ the¢ ¢ ¢ alternate¢ ¢ ¢ ¢ ¢ ¢ ¢ location¢ ¢ ¢ ¢ ¢ ¢ ¢ ID¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ @/bfactor=bfactor bfactor is the B-factor UCSF Chimera was developed by the Computer Graphics Laboratory at the University of California, San Francisco, under support of NIH grant P41-RR01081. The software is @/color=color color is the atom-level color Molecule Model Attributes copyrighted and licensed by the Regents of the University of California. assignment Usage Description ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ @/drawMode=mode mode can be 0 (dot, as in #/color=color color is the model-level color assignment wireframe), 1 (sphere, as in #/display whether display is enabled at the model level CPK), 2 (endcap, as in stick), or 3 (ball, as in ball-and-stick) #/explicitHydrogens whether the model has hydrogen atoms