represent ( style,  sel='sel' )

surfaceDelete ( category,  sel='sel' )

chain ( *args,  *kw )

show ( sel='sel',  asChain=0 )

move (
        x=0,
        y=0,
        z=0,
        frames=None,
        )

focus ( sel='sel' )

Window/cofr about displayed part of selection

modeldisplay ( sel='sel' )

modelcolor ( color,  sel='sel' )

Change model color

linewidth ( width,  sel='sel' )

unribbon ( sel='sel' )

ksdssp (
        sel='sel',
        energy=None,
        helixLen=None,
        strandLen=None,
        infoFile=None,
        )

swapres (
        newRes,
        sel='sel',
        preserve=0,
        bfactor=None,
        )

ribrepr ( style,  sel='sel' )

setDc_color ( color )

rlabel ( sel='sel' )

Display residue information as part of one atom label

surfaceNew (
        category,
        sel='sel',
        models=None,
        )

ribcolor ( color,  sel='sel' )

Change ribbon color

surfaceCategory ( category,  sel='sel' )

save ( filename )

evalSpec ( spec )

undistance ( sel='sel' )

Remove distance monitor

ribbackbone ( sel='sel' )

surfacetransparency ( val,  sel='sel' )

rotation ( sel='sel',  reverse=False )

matrixget ( fileName )

rmsd ( f,  t )

vdwdensity ( density,  sel='sel' )

Change vdw surface point density

windowsize ( width,  height )

setBg_color ( color )

unvdw ( sel='sel' )

Hide point vdw surface of atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is displayed.

rock (
        axis,
        magnitude=90,
        frequency=60,
        frames=-1,
        )

colordef ( color,  target )

Define RGB(A) color

bond ( sel='sel' )

textureUse ( name )

version ()

thickness ( delta,  frames=None )

freeze ()

Stop all motion

undisplay ( sel='sel' )

Undisplay atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is undisplayed.

close ( model,  subid=None )

ribbon ( sel='sel' )

Display residue as ribbon

rangeColor (
        attrName,
        colorItems,
        wayPoints,
        noValue,
        sel='#',
        )

color atom parts by attribute

attrName is a residue or atom attribute name. It can be prepended with atom. or residue. to resolve ambiguity if necessary. Otherwise, residue-level attributes win "ties".

colorItems is a comma-separated string of items to color (labels, surfaces, etc., as per the color command) or an empty string (color everything). In addition to the color command characters, the character r means to color ribbons.

wayPoints is a sequence of value/color tuples describing the color range layout. The values can be max, min, mid or numeric.

noValue is the color to apply to items missing the attribute. A value of None means to leave them unchanged.

scale ( s,  frames=None )

section ( delta,  frames=None )

label ( sel='sel',  warnLarge=0 )

Add label to selected atoms

textureMap ( **kw )

labelopt ( opt,  value )

change label display options

x3dSave ( filename )

unlabel ( sel='sel' )

Add label to selected atoms

deleteAtomsBonds ( atoms=[],  bonds=[] )

General utility functions

convertColor ( color )

ribscale ( name,  sel='sel' )

wait ( frames=-1 )

objdisplay ( sel='sel' )

pdbrun (
        cmd,
        all=0,
        conect=0,
        nouser=0,
        noobj=0,
        nowait=0,
        surface=0,
        mark=None,
        viewer=None,
        )

longbond (
        ratio=2.5,
        length=None,
        sel='sel',
        )

addaa ( args )

add an amino acid to the last residue in a chain

chimeraSelect ( sel='sel' )

color ( color,  sel='sel' )

Change atom color

pop ( frames=None,  mode='linear' )

unbondcolor ( sel='sel' )

unribbackbone ( sel='sel' )

open (
        filename,
        filetype=None,
        model=chimera.OpenModels.Default,
        noprefs=False,
        )

select ( sel='sel' )

Make selected models active

unclip ( plane )

unvdwdefine ( sel='sel' )

Revert to default VDW radii

chirality ( sel='sel' )

window ( sel='sel' )

Recompute window parameters

unsetAutocolor ()

unrlabel ( sel='sel' )

Do not display residue information as part of any atom label

surfacecolormode ( style,  sel='sel' )

namesel ( selName=None )

matrixcopy ( f,  t )

copy (
        printer=None,
        file=None,
        format=None,
        viewer=None,
        supersample=None,
        raytrace=False,
        rtwait=None,
        rtclean=None,
        )

brotation ( sel='sel' )

Setup backwards rotation

uncofr ()

reset (
        name='default',
        frames=None,
        mode='linear',
        )

distance ( sel='sel' )

Monitor distance between exactly two atoms

unsurface ( sel='sel' )

bondrepr ( style,  sel='sel' )

align ( sel )

savepos ( name='default' )

unribcolor ( which,  sel='sel' )

Clear ribbon color

match (
        f,
        t,
        selected=False,
        iterate=None,
        minPoints=1,
        )

Superposition the two specified sets of atoms ("from" and "to")

if selected is true, transform all active models, not just the from model.

if iterate is not None or False, the matching will iterate (pruning poorly-matching atom pairs at each pass) until no pair distance exceeds the value assigned to iterate

minPoints is the minimum number of points from each model to match. If fewer are specified (or, due to iterate, you go below the number), then TooFewAtomsError is raised.

unlongbond ()

surfacerepresent ( style,  sel='sel' )

matrixset ( fileName )

display ( sel='sel' )

Display atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is displayed.

delete ( sel='sel' )

Delete atoms

clip (
        plane,
        delta,
        frames=None,
        )

surface ( atomSpec='sel',  category='main' )

textureNew ( name,  numColors=5 )

unscale ()

getcrd ( sel='sel' )

Print the coordinates of selected atoms

rainbow ( sel='sel',  **kw )

Color selected models in rainbow pattern

vdw ( sel='sel' )

Display point vdw surface of atoms

Atoms specification may come from either a selection or an osl string. If no atom specification is supplied, the current selection is displayed.

angle ( sel='sel' )

Report angle between three or four atoms

unsavepos ( name )

turn (
        axis,
        angle=3,
        frames=None,
        )

cofr ( where='report' )

unsetIndependent ()

unbond ( sel='sel' )

vdwdefine (
        radius,
        sel='sel',
        increment=False,
        )

Change vdw radius

write (
        writeModel,
        relModel,
        filename,
        allFrames=False,
        dispOnly=False,
        selOnly=False,
        format="pdb",
        )

write a PDB or Mol2 file

write coordinates relative to relModel position. If relModel is None, write current coordinates.

allFrames controls whether all frames of a trajectory are written out or just the current frame

dispOnly, if true, means to write only displayed atoms

selOnly, if true, means to write only selected atoms

format should be "pdb" or "mol2"

unsetAttr (
        level,
        name,
        sel='sel',
        )

bondcolor ( color,  sel='sel' )

roll (
        axis,
        angle=3,
        frames=-1,
        )

setAutocolor ()

setAttr (
        level,
        name,
        val,
        sel='sel',
        )

uncolor ( which,  sel='sel' )

Clear atom color

unchimeraSelect ( sel='sel' )

bonddisplay ( mode,  sel='sel' )

unobjdisplay ( sel )

setIndependent ()

model ( n )

stereo ( mode )

unmodeldisplay ( sel='sel' )

center ( sel='sel' )

unselect ( sel='sel' )

Make selected models inactive

textureColor ( index,  color )

tColor ( index,  sel='sel' )

push ()

MidasError

TooFewAtomsError

ChimeraExtension.py

addAA.py

chiral.py

gui.py

midas_rainbow.py

midas_text.py

midas_ui.py