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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
• 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

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
• 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
• 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
• 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
• 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
• Surface
  To change the probe radius other than default 1.4 Å, you need to change the solvent radius, say, 1.6 Å:
  7 KB (1,009 words) - 09:22, 24 October 2016