use help to see description within PyMOL
____________ USAGE: fast_sym selection,cutoff=4.0,delete_sym=1
selection: object for symmetry calculation
cutoff: distance cutoff
delete_sym: delete previous sym files ("s_*")
commands
USAGE: del_sym (This will deleta all s_* files)commands
USAGE:
del_enabled selection="obj" # delete all enabled objects
del_enabled "selections" # delete all enabled selections
del_enabled "all" # delete all enabled
commands
USAGE: new_name old,newcommands
USAGE: get_pdb_lines(selection="all",state="0",enabled="0")
PYMOL: get_pdb (selection),state
selection: object or selection
state: state
enabled: 1: get only enabled items
0: get all items
commands
USAGE: mse sele="r. MSE" stype=-1 ssurface=1
sele: selection : standard is "r. MSE"
stype: 1: set "sele" type from HETATM to ATOM
0: set "sele" type from ATOM to HETATM
-1: do nothing (standard)
ssurface: 1: set surface representation of "sele" to 1 (create surface) (standard)
2: set surface representation of "sele" to 2 (dont show but include)
0: set surface representation of "sele" to 0 (exclude from surface)
this is standard within pymol for MSE hetatm
-1: do nothing
ADDITIONAL: this can be also used to ignore different surface parts of other selectionscommands
USAGE: get_box(name="box",
selection="all",
cushion=0.0,
draw="full",
coord="None",
linewidth="1.0"
)
PYMOL: get_box name=box,selection=all,cushion=2.0,draw=full,coord=None,linewidth=1.0
name: name of the cgo box
selection: selection for min and max of box calculation
cushion : extend box with cushion in Angstroms each side
or each side separately by "(xcmin,ycmin,zcmin,xcmax,ycmax,zcmax)"
draw: lines: draw a box with lines
full: draw a full box with each side separated
to hide box walls separately
coord : if coord is given as "(xmin,ymin,zmin,xmax,ymax,zmax)"
selection will be ignored
linewidth: 1.0 : in case of box with lines define linewidth
commands
USAGE: get_axes(name="axes",origin="(0.0,0.0,0.0)",lenght="10.0",linewidth="1.0")
PYMOL: axes name="axes",origin="(0.0,0.0,0.0)",lenght=10.0,linewidth=1.0
name: name of object
origin: zero coordinates of axes or "box" for origin coordinates of selection min coordinates
lenght: lenght of axes
linewidth: thickness of axes
commands
USAGE: get_point(name="point",
coord="(0.0,0.0,0.0)",
radius="0.5",
atom="0")
PYMOL: get_point name="point", #Name of object
coord="(0.0,0.0,0.0)", #coord of object
radius="0.5", #radius of cgo
atom="0" #1: create dummy atom instead of cgo
state="new" #"new": create unique name if name already exists
commands
USAGE: get_atom(name="atom",coord="(0.0,0.0,0.0)")
PYMOL: get_atom name="atom",coord=(0.0,0.0,0.0)commands
USAGE: get_center selectioncommands
USAGE: get_center_atom(selection,[name="center"])
PYMOL: get_center_atom selection,[name=center])commands
USAGE: sidebar set,value
set:
"on" : set sidebar on
"off" : set sidebar off
"width": set sidebar to value
"size" : set hight of each sidebar entry
"overlayon": sidebar overlay on
"overlayoff": sidebar overlay off
value:
value : int : value of sidebar
commands
USAGE: get_plane(selection,name="plane",size=100,invert=0,sphere=1)
name : :name of the plane
selection: :selection containing three atoms
size : int :size of the plane
invert : int : 1: invert normal for lightning
0: do not invert normal
2: do not create normal
sphere : int : 1: draw spheres on edges of the plane
: 0: do not draw spheres
PYMOL: get_plane selection,name,size,invert,spherecommands
USAGE: polyala(selection=None,name=None)
selection: selection of residues
name: name of created polyalanine
if no name is given the original input
will be altered to polyalanine
PYMOL: get_polyala (selection),[name]
selection: selection of residues
name: name of created polyalanine
if no name is given the original input
will be altered to polyalanine
ADDITIONAL: if "name" is specified the structure looks wired because of the
lack of bonds between the altered alanine residues.
If you want to see the bonds you can save and reopen the struture.
(Pymol recognize the new bonds after loading)
commands
USAGE: his_handle(fromto="his2hid",selection="(sele)",hisH_dic=None)
fromto :"his2hid": HIS to HIP HID HIE
:"hid2his": HIS HIP HIE to HIS
selection:(sele)
hisH_dic: dictionary of his hydrogen naming convention
e.g. {"HID":["HD1","H0X"],
"HIE":["HE2","H01"]}
USAGE: get_sequence(selection="sele",selecting="residue",format="normal",name=None,wrap="60")
selection: sele : selection of residues or atoms.
selecting: residue: get all residues of selection
atom: get all atoms of selection
chain: get all chains of selection
name: None : name of selection for output
format: normal: object: chain: residue-residue number
fasta: amino acid one letter code in fasta format
pir: amino acid one letter code in pir format
modeller: amino acid one letter code in Modeller pir format
wrap: 60: for sequence output wrap at 60 residues
gap: 1: add gaps between selected amino acids
0: do not add gaps
gap_sign: - : char of gap
"lower": gap amino acids are written as lower case
PYMOL: get_sequence selection=sele,selecting=residue,format=normal,wrap=60,gap_sign=lower
commands
USAGE: bni_ray(width,name_png=None,dpi="300",width_unit="cm",**arg)
width: width of ray picture in defined units
width_unit: : unit of width
cm: centi meter
inch: inch
mm: milli meter
dots: (normal behaviour of ray)
dpi: 300:dots per inch (resolution)
name_png: ./1: write png file with name 1.png
arg: additinal arguments for ray
height: integer :{default: 0 (current)}
antialias: integer :{default: -1 (use antialias setting)}
angle: float :y-axis rotation for stereo image generation
{default: 0.0}
shift: float : x-axis translation for stereo image generation
{default: 0.0}
renderer: -1 :respectively
0 :default
1 :built-in
2 :pov-ray, or dry-run {default: 0}
async: 0 : do not run in background thread
1 : background thread
PYMOL: bni_ray width,name_png=None,dpi="300",width_unit="cm",**argcommands
USAGE: combine_sele(selections=None,check="enabled",name="sele")
selections: "sele1 sele2 sele3": add additinal selections
check: "enabled": add only enabled selections
"all": add all selections
"disabled": add only disabled selectins
-1: do not look for selections
name: sele: specify name of combined selection
PYMOL: combine_sele selections=None,check=-1,name="sele"commands
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