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  • Surface solvent
    ...ace_solvent''' setting controls whether the solvent accessible (on) or the solvent excluded (off) [[surface]] is shown. [[Image:Surface solvent OFF.jpg]]
    338 bytes (46 words) - 15:07, 5 September 2011
  • File:Surface solvent OFF.jpg
    (400 × 267 (63 KB)) - 19:39, 5 February 2009
  • File:Surface solvent ON.jpg
    (400 × 267 (66 KB)) - 19:40, 5 February 2009
  • Solvent radius
    This defines the solvent radius. Changing the solvent radius in PyMOL affects how PyMOL interprets [[Surface_solvent|surfaces]], The default solvent radius is 1.4 Angstroms.
    511 bytes (62 words) - 15:57, 17 April 2009
  • File:ErmC 2ERC surface solvent OFF.png
    (640 × 480 (145 KB)) - 19:04, 5 February 2009
  • File:ErmC 2ERC surface solvent ON.png
    [[Image:ErmC 2ERC surface solvent OFF.png]] [[Image:ErmC 2ERC surface solvent ON.png]]
    (640 × 480 (155 KB)) - 19:08, 5 February 2009

Page text matches

  • Solvent radius
    This defines the solvent radius. Changing the solvent radius in PyMOL affects how PyMOL interprets [[Surface_solvent|surfaces]], The default solvent radius is 1.4 Angstroms.
    511 bytes (62 words) - 15:57, 17 April 2009
  • Category talk:FAQ
    ...e, the common "Is the surface representation solvent-accessible surface or solvent/protein interface.")
    286 bytes (47 words) - 17:44, 28 June 2006
  • Surface solvent
    ...ace_solvent''' setting controls whether the solvent accessible (on) or the solvent excluded (off) [[surface]] is shown. [[Image:Surface solvent OFF.jpg]]
    338 bytes (46 words) - 15:07, 5 September 2011
  • File:ErmC 2ERC surface solvent ON.png
    [[Image:ErmC 2ERC surface solvent OFF.png]] [[Image:ErmC 2ERC surface solvent ON.png]]
    (640 × 480 (155 KB)) - 19:08, 5 February 2009
  • Protein contact potential
    ...point-charge one solvent radius *above* the protein surface, if we ignore solvent screening and only consider nearby atoms. My personal opinion is that this ...ties between the low-dielectric interior and the high-dielectric exterior (solvent region).
    2 KB (320 words) - 09:41, 24 June 2009
  • File:Ribbon hh1.png
    ...ce:''' Monika Martick, Tai-Sung Lee, Darrin M. York and William G. Scott, Solvent Structure and Hammerhead Ribozyme Catalysis, ''[http://sage.ucsc.edu/scottl
    (596 × 761 (158 KB)) - 23:37, 12 September 2008
  • Talk:Get area
    ...lly, flag ignore does what it should, but the previously magically ignored solvent molecules are now no longer magically ignored so need to be specifically ex ...yet for per-residue SASA, but I suspect that it also needs a "flag ignore, solvent" adding.
    859 bytes (139 words) - 18:12, 23 November 2021
  • Mesh mode
    mesh_mode 1 allows you to show meshes for hetero atom and solvent atom objects.
    307 bytes (40 words) - 17:20, 2 November 2007
  • DYNMAP
    * Visualize distribution of functional groups in a protein, their solvent accessibility and their spatial fluctuation
    633 bytes (82 words) - 00:43, 5 July 2007
  • H Add
    ...ential calculations and a combinatorial search. There's also the issue of solvent & counter-ions present in systems like aspartyl proteases with adjacent car
    892 bytes (122 words) - 10:47, 20 June 2009
  • Get area
    '''1''' = calculate '''solvent accessible surface''' area (SASA) | The solvent radius {default: 1.4}
    6 KB (871 words) - 18:12, 23 November 2021
  • User talk:Dambor
    ...automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is import
    1 KB (169 words) - 10:35, 28 June 2007
  • Caver
    ...automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is import
    1 KB (202 words) - 17:48, 27 July 2017
  • Displaying Biochemical Properties
    For a solvent accessible PSA approximation: remove solvent
    14 KB (2,294 words) - 03:57, 21 August 2014
  • Get sasa relative
    ...n.wikipedia.org/wiki/Relative_accessible_surface_area relative per-residue solvent accessible surface area] and optionally labels and colors residues.
    1,003 bytes (131 words) - 18:15, 23 November 2021
  • APBS Electrostatics Plugin
    The most common visualization is to show the solvent excluded surface. PyMOL uses the [[surface_ramp_above_mode|potential at the solvent accessible surface]]
    5 KB (725 words) - 04:07, 18 May 2023
  • AAindex
    Solvent-accessible surface coloring by [https://www.genome.jp/dbget-bin/www_bget?aa
    2 KB (254 words) - 12:23, 22 March 2021
  • Gallery
    remove solvent *[[Solvent]]
    21 KB (3,151 words) - 18:06, 10 February 2017
  • Flag
    | Solvent
    3 KB (382 words) - 04:44, 6 August 2020
  • Azahar
    ...ations to run, whether or not to use a SASA model to take into account the solvent contribution, and whether or not to start from a random conformation. ...F94 force field (as implemented on open-babel) and the contribution of the solvent is approximated using a SASA model (the validity of the SASA model for glyc
    6 KB (985 words) - 12:23, 8 June 2020

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