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  • Internal gui mode
    This sets how PyMOL renders the internal GUI & controls. The default setting, 0. ...e:Ig_mode1.png|internal_gui_mode, set to 1. Notice the coloring under the controls.
    514 bytes (76 words) - 02:16, 28 March 2014
  • Movie loop
    This setting controls whether or not PyMOL loops your movies.
    251 bytes (33 words) - 02:16, 28 March 2014
  • Min mesh spacing
    The [[min_mesh_spacing]] setting controls the spacing between lines of the molecular [[mesh]] representation.
    502 bytes (65 words) - 02:27, 28 May 2019
  • Surface solvent
    The '''surface_solvent''' setting controls whether the solvent accessible (on) or the solvent excluded (off) [[surface
    338 bytes (46 words) - 01:44, 28 March 2014
  • Transparency mode
    [[Transparency_mode]] controls how PyMOL handles transparent objects
    568 bytes (63 words) - 02:52, 25 July 2016
  • Ribbon Width
    '''ribbon_width''' controls how fat or skinny PyMOL draws the ribbons, when using '''show ribbons'''.
    361 bytes (48 words) - 19:10, 31 March 2014
  • Internal gui control size
    This sets how large the internal gui controls are. An internal GUI control is the button you click on to enable/disable
    540 bytes (79 words) - 03:06, 28 March 2014
  • Surface color
    '''surface_color''' controls the color of surfaces as drawn in PyMOL.
    610 bytes (80 words) - 02:39, 24 July 2017
  • Internal Gui
    There's a small vertical bar on the bottom left of the VCR-style controls -- drag this left or right to resize the internal gui. This may allow you
    450 bytes (74 words) - 03:06, 28 March 2014
  • Spec direct power
    This controls the direct specular power. Essentially, this is how strongly surfaces that
    711 bytes (100 words) - 01:44, 28 March 2014
  • Line width
    Controls the width that PyMOL draws lines.
    616 bytes (96 words) - 02:16, 28 March 2014
  • Cartoon round helices
    This setting controls the "roundness" of cartoon helices. The default value is "on"; turning this
    641 bytes (89 words) - 01:42, 28 March 2014
  • Stick nub
    The stick_nub setting controls the height of the cones at the end of the sticks in stick representation.
    672 bytes (96 words) - 01:44, 28 March 2014
  • Seq view gap mode
    The [[seq_view_gap_mode]] setting controls if gap indicators are displayed in the [[:Category:Seqeuence_Viewer|sequenc
    582 bytes (82 words) - 04:20, 4 February 2019
  • Label anchor
    [[Label_anchor]] is a new setting that controls onto which atoms residue labels will go. Selecting L > Label > Residues cr
    605 bytes (103 words) - 02:16, 28 March 2014
  • Surface smooth edges
    the '''surface_smooth_edges''' setting controls appearance of the surface edges.
    884 bytes (116 words) - 02:46, 3 April 2017
  • Ignore case chain
    The [[ignore_case_chain]] setting (default: '''off''') controls whether the '''chain''' and '''segi''' [[Selection Algebra|selection operat
    665 bytes (93 words) - 04:50, 11 December 2017
  • Jupyter
    ** [https://pypi.org/project/ipymol/ IPyMOL] controls a PyMOL instance via [[RPC]] ** [https://www.rdkit.org/docs/source/rdkit.Chem.PyMol.html RDKit] controls a PyMOL instance via [[RPC]]
    3 KB (392 words) - 03:43, 6 December 2021
  • Atom name wildcard
    This setting controls whether or not PyMOL will respect wildcards ("*"). PyMOL automatically dis
    873 bytes (138 words) - 04:50, 11 December 2017
  • Modevectors
    #This controls the base radius of the cone/arrow head in angstroms (Fig.3) #This controls the radius of the cylinders/arrow tails in angstroms (Fig.4)
    7 KB (1,130 words) - 02:16, 28 March 2014
  • Dots
    Controls the dot radius when ray tracing (that is, it is apparent only after the sce * dot_solvent, default is off. This setting controls whether the dots are representing the vdW surface; when the setting is on,
    2 KB (396 words) - 02:18, 28 March 2014
  • Surface proximity
    ...of atoms (not the entire molecule), then the [[surface_proximity]] setting controls whether triangles are shown which are between an included and an excluded a
    886 bytes (127 words) - 02:46, 3 April 2017
  • Opaque background
    This setting controls how PyMOL renders the background. If this opaque setting is '''on''' then
    866 bytes (133 words) - 02:16, 28 March 2014
  • Ray orthoscopic
    This setting controls whether ray-traced images are rendered with or without perspective. Note t
    1 KB (141 words) - 23:12, 7 April 2014
  • Assembly
    When loading '''mmCIF''' structure files, the [[assembly]] setting controls whether PyMOL loads the asymmetric unit (assembly="") or a biological unit
    1 KB (155 words) - 02:19, 19 September 2016
  • Stick ball
    The setting "stick_ball" controls whether bonded atoms are shown simply as joined sticks (set stick_ball, off
    963 bytes (152 words) - 01:44, 28 March 2014
  • Smooth
    * ends = 0 or 1: controls whether or not the end states are also smoothed using a weighted asymmetric
    1 KB (145 words) - 01:22, 19 October 2015
  • Pdb conect nodup
    The '''pdb_conect_nodup''' setting in pymol controls if duplicated connectivity record ([http://www.wwpdb.org/documentation/file
    1 KB (201 words) - 01:04, 19 October 2015
  • Pdb conect all
    When saving a PDB file, the [[pdb_conect_all]] settings controls whether PyMOL writes CONECT records for all bonds, or only for HETATM bonds
    1 KB (175 words) - 05:01, 16 November 2015
  • Window
    '''window''' controls the visibility of PyMOL's output window
    1 KB (149 words) - 03:15, 5 March 2018
  • Scene
    * '''view''' = 1 or 0: controls whether the view is stored {default: 1} * '''color''' = 1 or 0: controls whether colors are stored {default: 1}
    6 KB (867 words) - 06:32, 11 January 2016
  • Fetch Host
    The '''fetch_host''' setting controls from which PDB server you download files when using the [[fetch]] command.
    1 KB (204 words) - 04:50, 11 December 2017
  • Normalize ccp4 maps
    The [[normalize_ccp4_maps]] settings (default: '''on''') controls whether or not PyMOL normalizes the data from a ccp4 map file '''upon loadi
    1 KB (193 words) - 20:24, 9 July 2015
  • Cluster mols
    ...nd a user specified receptor. Additionally there are a number of keyboard controls for selecting and extracting compounds, as well as functionality for search This script also integrates keyboard controls which allows for WASD movement through the clusters as well as keyboard sho
    8 KB (1,334 words) - 18:29, 25 May 2022
  • Surface quality
    This controls how well PyMOL draws surfaces. Lower values, like 0, are rough surface app
    1 KB (182 words) - 03:27, 14 November 2016
  • Cif use auth
    ...ng '''mmCIF''' structure files, the [[cif_use_auth]] setting (default: on) controls whether the '''auth_*''' fields are used or not.
    2 KB (257 words) - 01:04, 19 October 2015
  • Ignore case
    ..._case]] setting (default: '''on''', ''except in PyMOL 1.8.0.0 - 1.8.0.4'') controls whether PyMOL does case sensitive matching of atomic identifiers and select
    2 KB (243 words) - 03:47, 7 March 2016
  • Mutagenesis
    the back-and-forth movie controls (lower right corner) to display (in white) each of the rotamers available f
    2 KB (287 words) - 02:21, 20 August 2018
  • Collada geometry mode
    '''Collada geometry mode''' controls the types of <code>geometry</code> elements used in [[COLLADA]] output. Di
    2 KB (333 words) - 21:08, 9 July 2015
  • 3d pdf
    toolbar, %same as `controls' toolbar, %same as `controls'
    5 KB (880 words) - 21:08, 9 July 2015
  • ListSelection2
    * '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (
    3 KB (399 words) - 23:33, 26 May 2014
  • Spectrum
    ::integer: controls whether coloring is applied per-residue {default: 0}
    4 KB (522 words) - 02:11, 24 November 2019
  • OLD TOPTOC
    ## [[Mouse_Controls|Mouse Controls]]
    4 KB (451 words) - 02:16, 28 March 2014
  • TOPTOC
    ## [[Mouse_Controls|Mouse Controls]]
    6 KB (682 words) - 21:17, 28 March 2014
  • Command Line Options
    -h generic helper application (no controls, no feedback)
    5 KB (729 words) - 04:31, 26 June 2017
  • DistancesRH
    The script also runs a number of controls to verify that inputs and outputs exists/are suitable.
    8 KB (1,290 words) - 23:33, 26 May 2014
  • Label
    The [[Label]] command controls how PyMOL draws text labels for PyMOL objects.
    8 KB (1,237 words) - 03:04, 6 February 2017
  • Making Movies
    ...e original quality and maintaining small file sizes, however it lacks play controls. With skillful use of frame delays during the generation of the Gif it is p
    7 KB (1,247 words) - 02:16, 28 March 2014
  • Dehydron
    * Desolvatation sphere radius: this parameter controls the radius of the two spheres centred at the Cα carbon of the donor and ac
    10 KB (1,489 words) - 19:27, 29 May 2018
  • Practical Pymol for Beginners
    In the lower-right corner of the Viewer, next to the animation controls, is an '''S''' button (not to be confused with the '''S'''how button in the
    12 KB (1,971 words) - 02:46, 3 April 2017

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