None
None
None
None
DESCRIPTION
"aaindex" looks up the Amino Acid Index from
http://www.genome.jp/aaindex/
for the given key and assignes b-factors to the given selection. Unknown
residues get the average index value assigned.
USAGE
aaindex2b [key [, selection]]
ARGUMENTS
key = string: Key of AAindex entry
selection = string: atoms to assign b-factors {default: (all)}
EXAMPLE
# Hydropathy index by Kyte-Doolittle
aaindex2b KYTJ820101
spectrumany b, white yellow forest
show surface
DESCRIPTION
Potential of Mean Force
ARGUMENTS
key = string: aaindex key
cutoff = float: distance cutoff {default: 7.0}
cutoff = (float, float): distance shell
selection1 = string: atom selection {default: (name CB)}
selection2 = string: atom selection {default: selection1}
NOTES
Does also support a list of keys and a list of cutoffs to deal with
multiple distance shells.
EXAMPLES
# distance dependent c-beta contact potentials
pmf SIMK990101, 5, /2x19//A//CB
pmf SIMK990102, [5, 7.5], /2x19//A//CB
pmf [SIMK990101, SIMK990102, SIMK990103], [0, 5, 7.5, 10], /2x19//A//CB
# interface potential
sidechaincenters 2x19_scc, 2x19
pmf KESO980102, 7.0, /2x19_scc//A, /2x19_scc//B
distance /2x19_scc//A, /2x19_scc//B, cutoff=7.0
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for helices and gives slightly different results than loop_orientation.
Averages direction of C(i)->O(i) bonds.
USAGE
helix_orientation selection [, visualize [, sigma_cutoff]]
ARGUMENTS
selection = string: atom selection of helix
visualize = 0 or 1: show fitted vector as arrow {default: 1}
sigma_cutoff = float: drop outliers outside
(standard_deviation * sigma_cutoff) {default: 1.5}
SEE ALSO
angle_between_helices, helix_orientation_hbond, loop_orientation, cafit_orientation
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for alpha helices and gives slightly different results than
helix_orientation. Averages direction of O(i)->N(i+4) hydrogen bonds.
USAGE
helix_orientation selection [, visualize [, cutoff]]
ARGUMENTS
cutoff = float: maximal hydrogen bond distance {default: 3.5}
SEE ALSO
helix_orientation
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize]
SEE ALSO
helix_orientation
DESCRIPTION
Get the center and direction of a peptide by least squares
linear fit on CA atoms.
USAGE
cafit_orientation selection [, visualize]
NOTES
Requires python module "numpy".
SEE ALSO
helix_orientation
DESCRIPTION
Calculates the angle between two helices
USAGE
angle_between_helices selection1, selection2 [, method [, visualize]]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: function to calculate orientation {default: helix_orientation}
or int: 0: helix_orientation, 1: helix_orientation_hbond,
2: loop_orientation, 3: cafit_orientation
visualize = 0 or 1: show fitted vector as arrow {default: 1}
SEE ALSO
helix_orientation, helix_orientation_hbond, loop_orientation, cafit_orientation
None
DESCRIPTION
Set surface (or other) transparency for each atom scaled by b-factor.
Does not work for all, but for some transparency settings (for example
transparency, sphere_transparency)
ARGUMENTS
selection = string: atom selection {default: all}
setting = string: setting name {default: transparency}
minimum = float: b-factor range minimum {default: automatic}
maximum = float: b-factor range maximum {default: automatic}
var = string: numeric atomic property like b or q {default: b}
SEE ALSO
spectrum, cartoon putty
DESCRIPTION
Draws a plane across the backbone for a selection
ARGUMENTS
selection = string: protein object or selection {default: (all)}
color = string: color name or number {default: white}
transp = float: transparency component (0.0--1.0) {default: 0.0}
state = integer: object state, 0 for all states {default: 1}
NOTES
You need to pass in an object or selection with at least two
amino acids. The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
None
None
None
None
DESCRIPTION
Calculates the center of mass
Author: Sean Law
Michigan State University
slaw (at) msu . edu
None
Create a CGO circle
PARAMS
x, y, z
X, Y and Z coordinates of the origin
r
Radius of the circle
cr, cg, cb
Color triplet, [r,g,b] where r,g,b are all [0.0,1.0].
w
Line width of the circle
RETURNS
the CGO object (it also loads it into PyMOL, too).
circleSelection -- draws a cgo circle around a given selection or object
PARAMS
selName
Name of the thing to encircle.
r
Radius of circle.
DEFAULT: This cript automatically defines the radius for you. If
you select one atom and the resultant circle is too small, then
you can override the script's calculation of r and specify your own.
cr, cg, cb
red, green and blue coloring, each a value in the range [0.0, 1.0]
RETURNS
The circle object.
DESCRIPTION
Create a CGO arrow between two picked atoms.
ARGUMENTS
atom1 = string: single atom selection or list of 3 floats {default: pk1}
atom2 = string: single atom selection or list of 3 floats {default: pk2}
radius = float: arrow radius {default: 0.5}
gap = float: gap between arrow tips and the two atoms {default: 0.0}
hlength = float: length of head
hradius = float: radius of head
color = string: one or two color names {default: blue red}
name = string: name of CGO object
None
DESCRIPTION
Generates an animated flowing mesh object using the points provided
or the current view. The shape is affected substantially by the arguments!
USEAGE
cgo_grid [ pos1 [, pos2 [, pos3 [, length_x [, length_z
[, npoints_x [, npoints_z [, nwaves_x [, nwaves_z
[, offset_x [, offset_z [, gain_x [, gain_z [, thickness
[, color [, nstates [, startframe [, endframe [, mode
[, view [, name [, quiet ]]]]]]]]]]]]]]]]]]]]]]
EXAMPLE
cgo_grid view=1
ARGUMENTS
pos1 = single atom selection (='pk1') or list of 3 floats {default: [0,0,0]}
pos2 = single atom selection (='pk2') or list of 3 floats {default: [1,0,0]}
pos3 = single atom selection (='pk3') or list of 3 floats {default: [0,0,1]}
--> the plane is defined by pos1 (origin) and vectors to pos2 and pos3, respectively
length_x = <float>: length of membrane {default: 30}
length_z = <float>: length of membrane {default: ''} # same as length_x
npoints_x = <int>: number of points(lines) along x-direction
{default: ''} #will be set to give a ~1 unit grid
npoints_z = <int>: number of points(lines) along z-direction
{default: ''} #will be set to give a ~1 unit grid
{minimum: 1 # automatic}
nwaves_x = <float>: number of complete sin waves along object x-axis
{default: 2}
nwaves_z = <float>: number of complete sin waves along object z-axis
{default: ''} # same as nwaves_x
define separately to adjust number of waves in each direction
offset_x = <float> phase delay (in degrees) of sin wave in x-axis
can be set to affect shape and starting amplitude {default: 0}
offset_z = <float> phase delay (in degrees) of sin wave in z-axis
can be set to affect shape and starting amplitude
{default: ''} # same as offset_x
offset_x and offset_z can be used together to phase
otherwise identical objects
gain_x = <float>: multiplication factor for y-amplitude for x-direction
{default: 1}
gain_z = <float>: multiplication factor for y-amplitude for z-direction
{default: ''} #=gain_x
thickness = <float>: line thickness {default: 2}
color = color name <string> (e.g. 'skyblue') OR
rgb-value list of 3 floats (e.g. [1.0,1.0,1.0]) OR
{default: ''} // opposite of background
input illegal values for random coloring
nstates = <int>: number of states; {default: 60}
this setting will define how many states
the object will have (per wave) and how fluent and fast the
animation will be.
Higher values will promote 'fluent' transitions,
but decrease flow speed.
Note: Frame animation cycles thought the states one at a time
and needs to be set accordingly. Can also be used to phase
otherwise identical objects.
Set to 1 for static object {automatic minimum}
startframe: specify starting frame <int> or set (='') to use current frame
set to 'append' to extend movie from the last frame {default: 1}
endframe: specify end frame <int> or set (='') to use last frame
if 'append' is used for startframe,
endframe becomes the number of frames to be appended instead
{default: 1}
Note: if start- and endframe are the same, movie animation will
be skipped, the object will be loaded and can be used afterwards
mode: defines positioning {default: 0}:
0: pos1 is center
1: pos1 is corner
view {default: 0}:
'0': off/ uses provided points to create CGO
'1': overrides atom selections and uses current orienatation for positioning
- pos1 = origin/center
- pos2 = origin +1 in camera y
- pos3 = origin +1 in camera z
name: <string> name of cgo object {default: ''} / automatic
quiet: <boolean> toggles output
None
DESCRIPTION
Align two structures and show the structural deviations in color to more
easily see variable regions.
Colors each mobile/target atom-pair by distance (the name is a bit
misleading).
Modifies the B-factor columns in your original structures.
ARGUMENTS
mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
doAlign = 0 or 1: Superpose selections before calculating distances
{default: 1}
doPretty = 0 or 1: Show nice representation and colors {default: 1}
EXAMPLE
fetch 1ake 4ake, async=0
remove chain B
colorbyrmsd 1ake, 4ake
DESCRIPTION
Create a cube representation CGO for all atoms in selection.
ARGUMENTS
selection = string: atom selection {default: all}
name = string: name of CGO object to create
state = int: object state {default: 0 = all states}
scale = float: scaling factor. If scale=1.0, the corners of the cube will
be on the VDW surface of the atom {default: 0.5}
atomcolors = 0/1: use atom colors (cannot be changed), otherwise
apply one color to the object (can be changed with color command)
{default: 1}
SEE ALSO
tetrahedra
DESCRIPTION
Create a tetrahedra representation CGO for all atoms in selection.
SEE ALSO
cubes
None
None
None
None
DESCRIPTION
distancetoatom.py
Described at: http://www.pymolwiki.org/Distancetoatom
Prints all distanced between the specified atom/coordinate/center
and all atoms within cutoff distance that are part of the selection.
All coordinates and distances can be saved in a csv-style text file report
and can be appended to a (custom) atom property, if defined.
USAGE
distancetoatom [ origin [, cutoff [, filename [, selection
[, state [, property_name [, coordinates [, decimals [, sort
[, quiet ]]]]]]]]]]
ARGUMENTS
NAME TYPE FUNCTION
origin: <list> defines the coordinates for the origin and can be:
<str> 1. a list with coordinates [x,y,z]
2. a single atom selection string {default='pk1'}
3. a multi-atom selection string (center will be used)
cutoff <float> sets the maximum distance {default: 10}
filename <str> filename for optional output report. {default=None}
set to e.g. 'report.txt' to create a report
(omit or set to '', None, 0 or False to disable)
selection <str> can be used to define/limit the measurment to specific
sub-selections {default='all'}
state <int> object state, {default=0} # = current
property_name <str> the distance will be stored in this property {p.dist}
set "" to disable
coordinates <int> toggle whether atom coordinated will be reported {0}
decimals <int> decimals for coordinates and distance:
default = 3 # = max. PDB resolution
sort <int> Sorting by distance?
1: ascending (default)
0: no sorting (by names)
-1: descending
quiet <bool> toggle verbosity
DESCRIPTION
Given selection, draw a grid box around it.
USAGE:
drawgridbox [selection, [nx, [ny, [nz, [padding, [lw, [r, [g, b]]]]]]]]
PARAMETERS:
selection, the selection to enboxen
defaults to (all)
nx, number of grids on axis X
defaults to 10
ny, number of grids on axis Y
defaults to 10
nz, number of grids on axis Z
defaults to 10
padding, defaults to 0
lw, line width
defaults to 2.0
r, red color component, valid range is [0.0, 1.0]
defaults to 1.0
g, green color component, valid range is [0.0, 1.0]
defaults to 1.0
b, blue color component, valid range is [0.0, 1.0]
defaults to 1.0
RETURNS
string, the name of the CGO box
NOTES
* This function creates a randomly named CGO grid box. The user can
specify the number of grids on X/Y/Z axis, the width of the lines,
the padding and also the color.
DESCRIPTION
Create a nucleic acid base "block" cartoon with DSSR.
Requires the "x3dna-dssr" program, available from http://x3dna.org/
USAGE
dssr_block [ selection [, state [, block_file [, block_depth
[, block_color [, name [, exe ]]]]]]]
ARGUMENTS
selection = str: atom selection {default: all}
state = int: object state (0 for all states) {default: -1, current state}
block_file = face|edge|wc|equal|minor|gray: Corresponds to the --block-file
option (see DSSR manual). Values can be combined, e.g. "wc-minor".
{default: face}
block_depth = float: thickness of rectangular blocks {default: 0.5}
block_color = str: Corresponds to the --block-color option (new in DSSR
v1.5.2) {default: }
name = str: name of new CGO object {default: dssr_block##}
exe = str: path to "x3dna-dssr" executable {default: x3dna-dssr}
EXAMPLE
fetch 1ehz, async=0
as cartoon
dssr_block
set cartoon_ladder_radius, 0.1
set cartoon_ladder_color, gray
set cartoon_nucleic_acid_mode, 1
# multi-state
fetch 2n2d, async=0
dssr_block 2n2d, 0
set all_states
# custom coloring
fetch 1msy, async=0
dssr_block block_color=N red | minor 0.9 | major yellow
DESCRIPTION
Make 'dynamic' mesh from volumetric data such as electron density map.
The mesh will dynamically follow the center of the view.
Contour level of isomesh can be changed by PageDown and PageUp keys.
NOTE: Crystallographic operations can be applied to the map.
USAGE
dynamic_mesh map_name [, level [, radius [, name [, sym_source ]]]]
ARGUMENTS
map_name = string: name of volumetric object(map) to display
level = float: contour level of isomesh {default: 1.0}
radius = float: radius of isomesh around the center of the view {default: 8}
name = string: name of mesh object {default: dynamic_mesh}
sym_source = string: name of object from which symmetry
information is derived {default: map_name}
EXAMPLE
fetch 1hwk, async=0
fetch 1hwk, 1hwk_map, type=2fofc, async=0
dynamic_mesh 1hwk_map
SEE ALSO
isomesh
DESCRIPTION
Calculates the integer elbow angle of an antibody Fab complex and
optionally draws a graphical representation of the vectors used to
determine the angle.
ARGUMENTS
obj = string: object
light/heavy = strings: chain ID of light and heavy chains, respectively
limit_l/limit_h = integers: residue numbers of the last residue in the
light and heavy chain variable domains, respectively
draw = boolean: Choose whether or not to draw the angle visualization
REQUIRES: com.py, transformations.py, numpy (see above)
None
DESCRIPTION
Like "intra_fit", but for multiple objects instead of
multiple states.
ARGUMENTS
selection = string: atom selection of multiple objects {default: all}
reference = string: reference object name {default: first object in selection}
method = string: alignment method (command that takes "mobile" and "target"
arguments, like "align", "super", "cealign" {default: align}
... extra arguments are passed to "method"
SEE ALSO
alignto, cmd.util.mass_align, align_all.py from Robert Campbell
Adapted from Jason Vertrees https://pymolwiki.org/index.php/FindSurfaceResidues
DESCRIPTION
Finds those atoms on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
USAGE
findSurfaceAtoms [ selection, [ cutoff ]]
SEE ALSO
findSurfaceResidues
DESCRIPTION
Calculates a surface charge at entered pH. Also allows for the charge of an unfolded protein to be calculated.
USAGE
findSurfaceCharge [pH, [folded, [selection ,[cutoff]]]]
ARGUMENTS
pH = The pH value to estimate a surface charge at
folded = Whether the protein is folded (True) or denatured (False)
selection = string: object or selection in which to find exposed
residues {default: empty string - all objects}
cutoff = float: cutoff of what is exposed or not {default: 2.5 Ang**2}
RETURNS
A printout of the estimated surface charge at a given pH
DESCRIPTION
Finds those atoms on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
USAGE
findSurfaceAtoms [ selection, [ cutoff ]]
SEE ALSO
findSurfaceResidues
DESCRIPTION
Finds those residues on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
USAGE
findSurfaceResidues [ selection, [ cutoff, [ doShow ]]]
ARGUMENTS
selection = string: object or selection in which to find exposed
residues {default: all}
cutoff = float: cutoff of what is exposed or not {default: 2.5 Ang**2}
RETURNS
(list: (chain, resv ) )
A Python list of residue numbers corresponding
to those residues w/more exposure than the cutoff.
DESCRIPTION:
Given a sequence/regex to find, select those matching amino acids in the
protein.
USAGE:
findseq needle, [haystack[, selName[, het[, matchMode]]]]
PARAMS:
needle (string)
the sequence of amino acids to match and select
in the haystack. This can be a sequence of amino
acids, or a string-style regular expression. See
examples.
haystack (string; PyMOL object or selection; defaults to *)
name of the PyMOL object/selection in which
to find the needle.
selName (string; defaults to None)
This is the name of the selection to return. If selName
is left blank (None), then the selection name will be
foundSeqXYZ where XYZ is some random number; if selName is
"sele" the usual PyMOL "(sele)" will be used; and, lastly,
if selName is anything else, that name will be used verbatim.
het (0 or 1; defaults to 0)
This boolean flag allows (1) or disallows (0) heteroatoms
from being considered.
matchMode (first/all/chain; defaults to "all")
Subsequences or motifs might be repeated, this controls how we
consider multiple matches. Options are:
- 'first': Return the first match found in each object.
- 'chain': Return the first match found in each chain.
- 'all': Return all matches found in all chains.
RETURNS:
a newly created selection with the atoms you sought.
EXAMPLE:
# find SPVI in 1h12, foundSeqXYZ as return name
findseq SPVI, 1h12
# find FATEW and make it (sele).
findseq FATEW, 1g01, sele
# find the regular expression GMS.*QWY in 1a3h
# and put the return value in (sele).
fetch 1a3h
# this ends up finding the sequence, GMSSHGLQWY
findseq GMS.*QWY, 1a3h, sele
DESCRIPTION
"flatten_obj" combines multiple objects or states into a single object,
renaming chains where required
USAGE
flatten_obj name, selection[, state[, rename[, quiet[, chain_map]]]]
ARGUMENTS
name = a unique name for the flattened object {default: flat}
selection = the set of objects to include in the flattening. The selection
will be expanded to include all atoms of objects. {default: all}
state = the source state to select. Use 0 or -1 to flatten all states {default: 0}
rename = The scheme to use for renaming chains: {default: 0}
(0) preserve chains IDs where possible, rename other chains
alphabetically
(1) rename all chains alphabetically
(2) rename chains using the original chain letter, object name, and state
quiet = If set to 0, print some additional information about progress and
chain renaming {default: 1}
chain_map = An attribute name for the 'stored' scratch object. If
specified, `stored.<chain_map>` will be populated with a dictionary
mapping the new chain names to a tuple giving the originated object,
state, and chainID. {default: ""}
NOTES
Like the select command, if name is omitted then the default object name
("flat") is used as the name argument.
Chain renaming is tricky. PDB files originally limited chains to single
letter identifiers containing [A-Za-z0-9]. When this was found to be
limiting, multi-letter chains (ideally < 4 chars) were allowed. This is
supported as of PyMOL 1.7. Earlier versions do not accept rename=2, and
will raise an exception when flattening a structure with more than 62
chains.
EXAMPLES
flatten_obj flat, nmrObj
flatten_obj ( obj1 or obj2 )
SEE ALSO
split_states
DESCRIPTION
Creates fancy figures by introducing a focal blur to the image. The object
at the origin will be in focus.
AUTHOR
Jarl Underhaug
University of Bergen
jarl_dot_underhaug_at_gmail_dot_com
Updates by Jason Vertrees and Thomas Holder
USAGE
FocalBlur aperture=float, samples=int, ray=0/1, width=int, height=int
EXAMPELS
FocalBlur aperture=1, samples=100
FocalBlur aperture=2, samples=100, ray=1, width=600, height=400
DESCRIPTION
Formats bonds in aromatic or charged residues
EXAMPLE
frag PHE
format_bonds
USAGE
format_bonds [ selection [, bonds ]]
ARGUMENTS
selection: <str> input selection {default: 'all'}
bonds: <int> toogles format of bonds
1: single bonds (deactivates valence display)
2: regular double bonds (activates valence display)
>=3: delocalized (activates valence display)
None
DESCRIPTION:
returns a list of available pymol colors
USAGE:
get_colors [ selection [, quiet ]]
EXAMPLES:
get_colors # basic colors
get colors all # larger range with intermediates
DESCRIPTION:
returns a random color name available in pymol
! Requires get_colors !Indended mostly for use in Python
USAGE:
get_random_color [ selection [, quiet ]]
EXAMPLES:
# print a random color name:
get_random_color
# color object randomly:
fetch 1hpv, async=0
cmd.color(get_random_color())
DESCRIPTION
Get the list of pair items from distance objects. Each list item is a
tuple of (index1, index2, distance).
Based on a script from Takanori Nakane, posted on pymol-users mailing list.
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10143.html
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
state = integer: object state {default: 1}
selection = string: atom selection {default: all}
SEE ALSO
select_distances, cmd.find_pairs, cmd.get_raw_alignment
DESCRIPTION
Turns a distance object into a named atom selection.
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
name = a unique name for the selection {default: sele}
SEE ALSO
get_raw_distances
DESCRIPTION
"grepset" greps through the list of settings using a python
regular expression as defined in the 're' module.
It returns a list of settings/values matching the regexp.
No regexp returns every setting.
USAGE
grepset [regexp]
EXAMPLE
grepset line
grepset ray
grepset (^line|color$)
SEE ALSO
Python re module
DESCRIPTION
Create a box from the center coordinate of the box and the size of box
USAGE
run gridbox.py
1the simplest
gridbox center_x,center_y,center_z,size_x,size_y,size_z
2rename the box object
gridbox center_x,center_y,center_z,size_x,size_y,size_z,name,
3set the color of the box object
gridbox center_x,center_y,center_z,size_x,size_y,size_z,name,r1,g1,b1
4set the trasp of the box
gridbox center_x,center_y,center_z,size_x,size_y,size_z,name,r1,g1,b1,trasp
ps:the value of r1,g1,b1 trasp range is 0-1
trasp=1,no trasprent
DESCRIPTION
HBPLUS wrapper
DESCRIPTION
This script will draw the inertia tensor of the selection.
ARGUMENTS
selection = string: selection for the atoms included in the tensor calculation
name = string: name of the tensor object to be created {default: "tensor"}
state = int: state/model in the molecule object used in the tensor calculation
scaling = int {0, 1, or 2}: 0 for no scaling of the inertia axes, 1 for scaling
according to the molecular shape, 2 for scaling according to the eigenvalues
{default: 0}
EXAMPLE
PyMOL> run inertia_tensor.py
PyMOL> tensor molecule_object & i. 2-58+63-120 & n. n+ca+c, "tensor_model5_dom2", 5, 1
NOTES
Requires numpy.
DESCRIPTION
Opens a dialog with isolevel sliders for all isomesh and isosurface
objects in PyMOL.
DESCRIPTION
Load a stack of images as a map
ARGUMENTS
pattern = str: image filename or pattern
name = str: map object name to create
grid = float: grid spacing in Angstrom {default: 1.0}
channel = int: color channel for RGB images {default: 0}
normalize = 0 or 1: normalize data {default: 1}
extent = 3-float: (a,b,c) edge lengths in Angstrom, overwrites "grid"
arguments if given {default: }
EXAMPLES
load_img_stack img*.tif, extent=(21.0, 14.5, 18.2)
Authors Sean Law & Srinivasa
Michigan State University
slaw_(at)_msu_dot_edu
Editor Sacha Yee
USAGE
While in PyMOL
Parameter Preset Type Description
first_obj_frame Undefined String Object name of the first structure. The mode vector will propagate from this structure. Defined by user.
last_obj_frame Undefined String Object name of the last structure. The mode vector (arrow head) will end at this structure. Defined by user.
first_state 1 Integer Defines state of first object
last_state 1 Integer Defines state of last object
outname modevectors String Name of object to store mode vectors in.
head 1.0 Float Radius for the circular base of the arrow head (cone)
tail 0.3 Float Radius for the cylinder of the arrow tail (cylinder)
head_length 1.5 Float Length of the arrow head (from the base of the cone to the tip of cone)
head_rgb 1.0,1.0,1.0 String RGB colour for the arrow head.
tail_rgb 1.0,1.0,1.0 String RGB colour for the arrow tail.
cutoff 4.0 Float Skips mode vectors that do not meet the cutoff distance (in Angstroms).
skip 0 Integer Denotes how many atoms to skip. No arrows will be created for skipped atoms.
cut 0.0 Float Truncates all arrow tail lengths (without disturbing the arrow head) (in Angstroms).
atom CA String Designates the atom to derive mode vectors from.
stat show String Keeps track and prints statistics (total modevectors, skipped, cutoff).
factor 1.0 Float Multiplies each mode vector length by a specified factor.
Values between 0 and 1 will decrease the relative mode vector length.
Values greater than 1 will increase the relative mode vector length.
notail 0 Integer Hides tails and only uses cones (porcupine plot)
DESCRIPTION
Fades the color of representations in movies
#NB!: Defines and uses new color names using the selection name and frame numbers
USE
movie_color_fade startframe='', startcolor=red, endframe='', endcolor=green, selection=all
#defaults indicated
PARAMETERS
startframe, endframe = beginning and end movie frame for fading
startcolor, endcolor = coloring at start and end
selection: target selection
NB! startframe and endframe can be omitted or set='' to assign current and last frame respectively
EXAMPLES
##### 1. #####
fetch 1hpv, async=0
as cartoon
orient
color yellow
mset 1x120
movie_color_fade 1, yellow, 60, blue
movie_color_fade 60, blue, 120, yellow
#####
##### 2. #####
#repeat command and specify 'selection' to change multiple colors
fetch 1hpv, async=0
as cartoon
orient
color white
mset 1x60
movie_color_fade auto,white,auto,skyblue,ss s
movie_color_fade auto,white,auto,red,ss h
movie_color_fade auto,white,auto,grey,ss l+""
#####
SEE ALSO
mdo, mappend, set, movie_fade
DESCRIPTION
Fades representations in movies with their transparency settings.
USAGE
movie_fade setting, startFrame, startVal, endFrame, endVal [, selection ]
EXAMPLE
fetch 1rx1, async=0
as cartoon
show surface
mset 1x80
movie.roll
movie_fade transparency, 1, 0., 40, 1.
movie_fade transparency, 41, 1., 80, 0.
SEE ALSO
mdo, mappend, set
DESCRIPTION
Creates perpendicular planes
DESCRIPTION
Create a CGO plane from three atomic coordinates
USAGE
make_plane name, a1, a2, a3
where each atom is a standard PyMOL selection (defaults to pk1,pk2 and pk3)
DESCRIPTION
Create a CGO plane from three atomic coordinates
USAGE
make_plane name, l1, l2, l3
where each xys is a list with floats of x,y,z coordinates
DESCRIPTION
A function for plotting XPLOR NOE restraints on a structure
ARGUMENTS
filename = string: The filename of the NOE retraint file in XPLOR NIH format.
line_color = string: The color for the NOE lines. {default: yellow}
line_width = float: The thickness of the NOE lines. {default: 1.0}
advanced_coloring = color restraints by distance.
single = string: create a single object for all restraints.
aria = integer: Name NOEs after Aria IDs.
per_atom: Group NOEs on atom basis
per_residue: Group NOEs on residue basis (default)
NOE Restraint Format Example
assign (residue 5 and name HB#) (residue 21 and name HA) 3.0 0.7 0.7
EXAMPLE
PyMOL> plot_noe noe_short.tbl
DESCRIPTION
PoseView wrapper
http://www.biosolveit.de/poseview/
USAGE
poseview [ ligand [, protein [, width [, height [, exe [, state ]]]]]]
ARGUMENTS
ligand = string: atom selection {default: organic inorganic}
protein = string: atom selection {default: polymer}
width = int: image width {default: viewport width}
height = int: image height {default: viewport height}
filename = string: output PNG file name {default: temporary}
exe = string: path to executable {default: poseview}
SETUP
1) Put poseview executable to PATH (e.g. /usr/bin/poseview)
2) Set environment variable BIOSOLVE_LICENSE_FILE="/path/to/poseview.lic"
20110823
None
None
None
DESCRIPTION
Formats the passed object into secondary structure cartoon
USAGE
disp_ss [ selection [, colors [, only ]]]
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
colors='marine red white' <str> any three colors for: sheets, helices and loops
e.g. 'marine red white'
can also be set to either util.cbc, util.rainbow,
or util.chainbow (alone)
set='False' to supress coloring altogether, or enter False
for the coloring to be omitted, e.g. 'marine False green'
only <bool> if True will use show_as; else show
DESCRIPTION
Formats the passed object into ball and stick
USEAGE
disp_ball_stick [ selection [, hydrogens [, only ]]]
EXAMPLE
fetch 1hpv, async=0
disp_ball_stick
util.cbaw
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
hydrogens <int> -1: remove; 1: add; else: as is
only=False <bool> if True will use show_as; else show
see help disp_stick_ball
DESCRIPTION
Adds a mesh to the object
Has advanced coloring options and automatically accounts for the hydrogens
USEAGE
disp_mesh [ selection [, color_m [, hydrogens [, only [, limits]]]]]
disp_mesh selection=all, color_m=default
disp_mesh selection=all, color_m=white
disp_mesh selection=all, color_m=putty
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
color_m='default' <str> 'default': as current
'name': colors by color or ramp called name
'putty': b-factor on surface
hydrogens=0 <int> -1: remove; 1: add; else: as is
only=False <bool> if True will use show_as; else show
limits=5 <list or flaot>
applies only if color_m=='putty'
sets the b-factor range limits
<list> [min,max] # absolute values
<float> percentile cutoff (both sides) # relative for each protein
DESCRIPTION
Advanced surface representation (cf. examples)
USAGE
disp_surf [ selection [, color_s [, transparency [, hydrogens [, solvent [, ramp_above [, only [, limits]]]]]]]]
EXAMPLES
disp_surf # opaque surface with default colors
disp_surf all, white, 0.5 # half-transparent white surface
disp_surf all, putty # b-factor on surface
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
color_s='default' <str> 'default': as current
'name': colors by color or ramp called name
'putty': b-factor on surface (by resi)
transparency=0 <float> set surface transparency
hydrogens=0 <int> -1: remove; 1: add; else: as is
solvent=0 <int> defines 'surface_solvent'
ramp_above=1 <int> defines 'surface_ramp_above_mode'
only=False <bool> if True will use show_as; else show
limits=5 <list or flaot>
applies only if color_s=='putty'
sets the b-factor range limits
<list> [min,max] # absolute values
<float> percentile cutoff (both sides) # relative for each protein
DESCRIPTION
Formats the passed object into a Putty b-factor sausage
USEAGE
disp_putty [ selection ]
selection <str> input selection
limits=10 <list or flaot>
applies only if color_m=='putty'
sets the b-factor range limits (by protein)
<list> [min,max]
<float> percentile cutoff (both sides)
only=True <bool> if True will use show_as; else show
removeAlt -- remove all alternate location-atoms not of altloc "keep" from object.
input:
obj -- the object(s) to remove the atoms frmo
keep -- which type of alt loc to keep
output: none -- removes atoms
examples:
removeAlt # remove all altLocations that aren't altloc A
removeAlt pdbID, C # remove all but C altlocations from pdbID
DESCRIPTION
Set residue numbering (resi) based on connectivity.
ARGUMENTS
selection = string: atom selection to renumber {default: all}
start = integer: counting start {default: 1}
startsele = string: residue to start counting from {default: first in
selection}
None
None
None
DESCRIPTION
Save to MOPAC format
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: all}
zero = string: atoms to save with zero flag {default: none}
state = integer: state to save {default: -1 (current state)}
DESCRIPTION
Save in PDB format including ANISOU records.
SEE ALSO
save
DESCRIPTION
Dumps all settings with non-default values to ~/.pymolrc-settings.py
Feature Request: Save settings for later use - ID: 1009951
https://sourceforge.net/tracker/?func=detail&aid=1009951&group_id=4546&atid=354546
DESCRIPTION
Make named selections from SITE records.
ARGUMENTS
name = string: molecular object {default: all}
filename = string: PDB file name with SITE records {default: look in
current directory and fetch_path for <name>.pdb}
prefix = string: prefix for named selections {default: site_}
nice = 0 or 1: make colored sticks representation for sites {default :1}
None
DESCRIPTION
Visualize VDW clashes
ARGUMENTS
selection = string: atom selection {default: all}
name = string: name of CGO object to create {default: bump_check}
DESCRIPTION
Visualize interactions between receptor and ligand.
ARGUMENTS
recsel = string: atom selection of the receptor {default: "not hetatm"}
ligsel = string: atom selections of the ligand {default: "hetatm"}
cutoff = float: show as sticks all receptor residues within this distance from the ligand {default: 5.0}
DESCRIPTION
Color each state in a multi-state object different.
USAGE
spectrum_states [ selection [, representations [, color_list [, first [, last ]]]]]
ARGUMENTS
selection = string: object names (works with complete objects only)
{default: all}
representations = string: space separated list of representations
{default: cartoon ribbon}
color_list = string: space separated list of colors {default: blue cyan
green yellow orange red}
SEE ALSO
spectrum, spectrumany
DESCRIPTION
Define a color spectrum with as many color-stops as you like (at least 2).
USAGE
spectrumany expression, color_list [, selection [, minimum [, maximum ]]]
ARGUMENTS
expression = count, resi, b, q, or pc: respectively, atom count, residue
index, temperature factor, occupancy, or partial charge {default: count}
color_list = string: Space separated list of colors
... all other arguments like with `spectrum` command
EXAMPLE
spectrumany count, forest green yellow white
spectrumany b, red yellow white, (polymer), maximum=100.0
SEE ALSO
spectrum
Author Sean M. Law
University of Michigan
seanlaw_(at)_umich_dot_edu
USAGE
While in PyMOL
run spectrumbar.py
spectrumbar (RGB_Colors,radius=1.0,name=spectrumbar,head=(0.0,0.0,0.0),tail=(10.0,0.0,0.0),length=10.0, ends=square)
Parameter Preset Type Description
RGB_Colors [1.0,1.0,1.0] N/A RGB colors can be specified as a
triplet RGB value or as PyMOL
internal color name (i.e. red)
radius 1.0 float Radius of cylindrical spectrum bar
name spectrumbar string CGO object name for spectrum bar
head (0.0,0.0,0.0) float Starting coordinate for spectrum bar
tail (10.0,0.0,0.0) float Ending coordinate for spectrum bar
length 10.0 float Length of spectrum bar
ends square string For rounded ends use ends=rounded
Examples:
spectrumbar red, green, blue
spectrumbar 1.0,0.0,0.0, 0.0,1.0,0.0, 0.0,0.0,1.0
The above two examples produce the same spectrumbar!
spectrumbar radius=5.0
spectrumbar length=20.0
DESCRIPTION
"stereo_ray" ray-traces the current scene twice (separated by
a six-degree rotation around the y axis)
and saves a pair of images that can be combined in any image
manipulation software to form a stereoimage.
The first argument, the output file name, is mandatory.
The second and third arguments, the size of the image, are not.
If the width is given, the height will be calculated.
USAGE
stereo_ray filename [, width [, height]]
EXAMPLE
stereo_ray output, 1000, 600
stereo_ray secondImage.png
DESCRIPTION
Align copies of mobile to target with several alignment methods
ARGUMENTS
mobile = string: atom selection
target = string: atom selection
methods = string: space separated list of PyMOL commands which take
arguments "mobile" and "target" (in any order) {default: align super
cealign tmalign}
DESCRIPTION
TMalign wrapper
Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
http://zhanglab.ccmb.med.umich.edu/TM-align/
USAGE
tmalign mobile, target [, args [, exe ]]
ARGUMENTS
mobile, target = string: atom selections
args = string: Extra arguments like -d0 5 -L 100
exe = string: Path to TMalign executable {default: TMalign}
ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
at first TER record {default: 0}
SEE ALSO
tmscore, mmalign
DESCRIPTION
TMscore wrapper
Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710
http://zhanglab.ccmb.med.umich.edu/TM-score/
ARGUMENTS
mobile, target = string: atom selections
args = string: Extra arguments like -d 5
exe = string: Path to TMscore executable {default: TMscore}
ter = 0/1: If ter=0, then ignore chain breaks because TMscore will stop
at first TER record {default: 0}
SEE ALSO
tmalign, mmalign
DESCRIPTION
MMalign wrapper
Reference: S. Mukherjee and Y. Zhang, Nucleic Acids Research 2009; 37: e83
http://zhanglab.ccmb.med.umich.edu/MM-align/
SEE ALSO
tmalign, tmscore
DESCRIPTION
toGroup will take a multistate object and extract it
to a group with N objects all in state #1. It essentially
performs the following:
split_states myObj, prefix=somePrefix
group newGroup, somePrefix*
delete myObj
PARAMETERS:
groupName (string)
The name of the group to create
sel (string)
The name of the selection/object from which
to make the group
prefix (string)
The prefix of the names of each of split states.
For example, if your prefix is ''obj'' and is in
states 1 through 100 then the states will be labeled
obj1, obj2, obj3, ..., obj100.
delOrig (string/boolean)
If true then delete the original selection, otherwise not.
RETURN
Nothing, it makes a new group.
DESCRIPTION
Fetch feature list from uniprot.org and create named selections.
Requires residue numbering (resi) to match uniprot sequence!
ARGUMENTS
uniprot_id = string: UniProtKB name or accession
selection = string: atom selection {default: all}
withss = 0/1: update secondary structure {default: 0}
DESCRIPTION
Like "uniprot_features" but with automatic fetching of UniProtKB accession
and sequence mapping for given pdb_id from http://www.bioinf.org.uk/pdbsws/
ARGUMENTS
pdb_id = string: PDB accession ID
selection = string: atom selection {default: <pdb_id>, will be fetched if
no such object is loaded}
withss = 0/1: update secondary structure {default: 0}
DESCRIPTION
Visualize Xplor-NIH NOE violations.
ARGUMENTS
molecule = string: molecule on which to show the violations.
viol_file = string: Xplor-NIH .viol file that contains the violations to be visualized.
viol_class = string: NOE class in .viol file to show {default: None (means all NOE classes)}.
EXAMPLE
PyMOL> run viol_noes.py
PyMOL> viol_noes molecule, ./molecule.pdb.viol
NOTES
The NOE violations will be shown as distances between the relevant residues/atoms and colored according to the severity of violation (the closer to the blue end of the spectrum, the more severe the violation; to closer to the red end, the less severe the violation).
None
None