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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_orientationDESCRIPTION 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_orientationDESCRIPTION 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_orientationDESCRIPTION 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_orientationDESCRIPTION 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 -
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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) -
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NoneDESCRIPTION Calculates the center of mass Author: Sean Law Michigan State University slaw (at) msu . edu -
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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 -
NoneDESCRIPTION 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 -
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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 tetrahedraDESCRIPTION Create a tetrahedra representation CGO for all atoms in selection. SEE ALSO cubes -
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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) -
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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 findSurfaceResiduesDESCRIPTION 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 findSurfaceResiduesDESCRIPTION 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 "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) -
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DESCRIPTION: returns a list of available pymol colors USAGE: get_colors [ selection [, quiet ]] EXAMPLES: get_colors # basic colors get colors all # larger range with intermediatesDESCRIPTION: 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/[email protected]/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_alignmentDESCRIPTION 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 -
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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 -
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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" -
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NoneDESCRIPTION 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 showDESCRIPTION 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 showsee help disp_stick_ballDESCRIPTION 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 proteinDESCRIPTION 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 proteinDESCRIPTION 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} -
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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 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). -
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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 surfaceDESCRIPTION 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 -
findseq needle, haystack[, selName[, het[, firstOnly]]] -
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, mmalignDESCRIPTION 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, mmalignDESCRIPTION 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 -
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