Electrostatic potential maps: Difference between revisions
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It is revealing to visualize the distribution of electrostatic charges, [https://en.wikipedia.org/wiki/Electric_potential electrostatic potential], on molecular [https://en.wikipedia.org/wiki/Van_der_Waals_surface van der Waals surfaces]. Most protein-protein and protein-ligand interactions are largely electrostatic in nature, via hydrogen bonds and ionic interactions. Their strengths are modulated by the nature of the solvent: pure water or high ionic strength aqueous solution<ref>This opening paragraph was adapted from text authored by [[User:Karsten Theis]] in [[Jmol/Electrostatic potential]].</ref>. [[Missing residues and incomplete sidechains|Missing atoms or residues]], nearly universal in [[empirical models]], cause [[Missing_residues_and_incomplete_sidechains#Why_Missing_Residues_Matter|errors in the map]]. Therefore it is '''{{font color|red|crucial to use a model without missing atoms}}''', which could be an [[Missing_residues_and_incomplete_sidechains#AlphaFold_models_have_no_missing_atoms|AlphaFold model]]. | It is revealing to visualize the distribution of electrostatic charges, [https://en.wikipedia.org/wiki/Electric_potential electrostatic potential], on molecular [https://en.wikipedia.org/wiki/Van_der_Waals_surface van der Waals surfaces]. Most protein-protein and protein-ligand interactions are largely electrostatic in nature, via hydrogen bonds and ionic interactions. Their strengths are modulated by the nature of the solvent: pure water or high ionic strength aqueous solution<ref>This opening paragraph was adapted from text authored by [[User:Karsten Theis]] in [[Jmol/Electrostatic potential]].</ref>. Charged residues modulate enzyme efficiency over considerable distances<ref>PMID: 39928564</ref>. [[Missing residues and incomplete sidechains|Missing atoms or residues]], nearly universal in [[empirical models]], cause [[Missing_residues_and_incomplete_sidechains#Why_Missing_Residues_Matter|errors in the map]]. Therefore it is '''{{font color|red|crucial to use a model without missing atoms}}''', which could be an [[Missing_residues_and_incomplete_sidechains#AlphaFold_models_have_no_missing_atoms|AlphaFold model]]. | ||
While exploring a structure in [[FirstGlance in Jmol]], electrostatic potential maps can be generated with a few mouse clicks -- see [[#iCn3D via FirstGlance in Jmol|instructions below]]. | While exploring a structure in [[FirstGlance in Jmol]], electrostatic potential maps can be generated with a few mouse clicks -- see [[#iCn3D via FirstGlance in Jmol|instructions below]]. | ||
==Gallery== | ==Gallery== | ||
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{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
|[[Image:1bl8-ABC-chimerax-epm-330px.gif]] | |||
|[[Image:1bl8ABC-cap2-trimmed.gif]] | |[[Image:1bl8ABC-cap2-trimmed.gif]] | ||
| <big>'''Potassium channel'''</big> ([[1bl8]]). The electrostatic potential map shows '''{{Font color|red|negatively charged protein surface}}''' lining the channel containing '''{{Font color|#00b000|K<sup>+</sup> ions}}'''. | | <big>'''Potassium channel'''</big> ([[1bl8]]). The electrostatic potential map shows '''{{Font color|red|negatively charged protein surface}}''' lining the channel containing '''{{Font color|#00b000|K<sup>+</sup> ions}}'''. | ||
Map generated by [[iCn3D]] | <span style="font-size:200%;">←</span>Left: Map generated by [[ChimeraX]]<ref>Colors of the electrostatic potential map generated by ChimeraX were intensified by reducing the range from default -10 to 10 with the command "coulombic sel range -4,4".</ref>, see [[#ChimeraX|method]]. | ||
Right<span style="font-size:200%;">→</span>: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]]. | |||
Map generated from a PDB file from which one of the 4 chains was removed with a [[plain text editor]] to reveal the inside surface of the channel. | |||
'''Caution''': Map generated with [[1bl8]] which has, in each of the 3 chains, 3 Arginines and 1 Glutamic acid with [[Missing residues and incomplete sidechains#Incomplete Sidechains|incomplete sidechains]]. | |||
|} | |||
{| class="wikitable" | |||
|- | |||
|[[Image:1bl8-ABC-EPM-PyMOL-1.png|330px]] | |||
|[[Image:1bl8-ABC-EPM-PyMOL-2.png|330px]] | |||
| <big>'''Potassium channel'''</big> ([[1bl8]]). The electrostatic potential map shows '''{{Font color|red|negatively charged protein surface}}''' lining the channel containing '''{{Font color|#00b000|K<sup>+</sup> ions}}'''. | |||
Map generated by [[PyMOL]], see [[#PyMOL|method]]. | |||
Right<span style="font-size:200%;">→</span>: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]]. | |||
Map generated from a PDB file from which one of the 4 chains was removed with a [[plain text editor]] to reveal the inside surface of the channel. | |||
'''Caution''': Map generated with [[1bl8]] which has, in each of the 3 chains, 3 Arginines and 1 Glutamic acid with [[Missing residues and incomplete sidechains#Incomplete Sidechains|incomplete sidechains]]. | '''Caution''': Map generated with [[1bl8]] which has, in each of the 3 chains, 3 Arginines and 1 Glutamic acid with [[Missing residues and incomplete sidechains#Incomplete Sidechains|incomplete sidechains]]. | ||
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# Optionally, in iCn3D, Menu: Style, Background, White. | # Optionally, in iCn3D, Menu: Style, Background, White. | ||
# To spin, iCn3D Menu: View, Rotate, Auto Rotation. | # To spin, iCn3D Menu: View, Rotate, Auto Rotation. | ||
# See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]]. | |||
====In iCn3D==== | ====In iCn3D==== | ||
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# Menu (optional): Style, Background, White. | # Menu (optional): Style, Background, White. | ||
# To spin, Menu: View, Rotate, Auto Rotation. | # To spin, Menu: View, Rotate, Auto Rotation. | ||
# To remove the yellow selection halo, enter the command (in the slot at the bottom) "select sets nothing". | |||
To remove the yellow selection halo, enter the command (in the slot at the bottom) "select sets nothing". | # See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]]. | ||
===ChimeraX=== | ===ChimeraX=== | ||
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# After the surface appears, try the Lighting & Effects options in the ''Graphics'' tab. | # After the surface appears, try the Lighting & Effects options in the ''Graphics'' tab. | ||
# De-select with the checkbox in the Models box. | # De-select with the checkbox in the Models box. | ||
# To save an MP4 movie to the Desktop, click the ''Spin movie'' icon in the Home tab: [[Image:Chimerax-movie-icon.png|30px]] | |||
# See [[#Converting MOV or MP4 to GIF|Converting MP4 to GIF]]. | |||
===PyMOL=== | ===PyMOL=== | ||
[https://pymol.org PyMOL] has a license fee, but is free for students and educators. | [https://pymol.org PyMOL] has a license fee, but is free for students and educators. | ||
<ol> | |||
<li> Download and install PyMOL. | |||
<li> Enter command "fetch 1pgb". | |||
<ul> | |||
<li> The above command loads the asymmetric unit. Commands to load biological assembly 1: | |||
<li> fetch 7mgp, type=pdb1 | |||
<li> split_state 7mgp | |||
</ul> | |||
<li> Menu: All, Action, remove waters. | |||
<li> Menu: 1pgb, Action, generate, vacuum electrostatics, protein contact potential (local). For a biological assembly, it appears that you will have to repeat this command for every part. | |||
<li> Enter command "bg_color white". | |||
</ol> | |||
Optional: The probe radius used to generate the molecular surface can be changed, and the previously generated surface will immediately change. The command is "set solvent_radius, 1.2" (don't overlook the comma!). | Optional: The probe radius used to generate the molecular surface can be changed, and the previously generated surface will immediately change. The command is "set solvent_radius, 1.2" (don't overlook the comma!). | ||
===Converting MOV or MP4 to GIF=== | |||
Please see at FirstGlance in Jmol: [http://firstglance.jmol.org/videocapture.htm Video Capture & Conversion]. | |||
===Coloring Charged Atoms=== | ===Coloring Charged Atoms=== | ||