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]].

==Gallery==

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←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→: 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+ ions}}'''.

Map generated by [[PyMOL]], see [[#PyMOL|method]].

Right→: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]].

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# Optionally, in iCn3D, Menu: Style, Background, White.

# To spin, iCn3D Menu: View, Rotate, Auto Rotation.

# See [[#Converting MOV or MP4 to GIF|~~Converting~~ MOV or MP4 to GIF]].

# See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]].

====In iCn3D====

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# 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".

# See [[#Converting MOV or MP4 to GIF|~~Converting~~ MOV or MP4 to GIF]].

# See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]].

===ChimeraX===

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# 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 ~~MOV or~~ MP4 to GIF]].

# See [[#Converting MOV or MP4 to GIF|Converting MP4 to GIF]].

===PyMOL===

[https://pymol.org PyMOL] has a license fee, but is free for students and educators.

# Download and install PyMOL.

<ol>

# Enter command "fetch 1pgb".

<li> Download and install PyMOL.

# Menu: All, Action, remove waters.

<li> Enter command "fetch 1pgb".

# Menu: 1pgb, Action, generate, vacuum electrostatics, protein contact potential (local).

<ul>

# Enter command "bg_color white".

<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!).

Electrostatic potential maps: Difference between revisions

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@@ Line 1: / Line 1: @@
-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]].
 ==Gallery==
@@ Line 24: / Line 24: @@
 <span style="font-size:200%;">&larr;</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%;">&rarr;</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%;">&rarr;</span>: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]].
@@ Line 78: / Line 93: @@
 # Optionally, in iCn3D, Menu: Style, Background, White.
 # To spin, iCn3D Menu: View, Rotate, Auto Rotation.
-# See [[#Converting MOV or MP4 to GIF|Converting MOV or MP4 to GIF]].
+# See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]].
 ====In iCn3D====
@@ Line 90: / Line 105: @@
 # 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".
-# See [[#Converting MOV or MP4 to GIF|Converting MOV or MP4 to GIF]].
+# See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]].
 ===ChimeraX===
@@ Line 102: / Line 117: @@
 # 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 MOV or MP4 to GIF]].
+# See [[#Converting MOV or MP4 to GIF|Converting MP4 to GIF]].
 ===PyMOL===
 [https://pymol.org PyMOL] has a license fee, but is free for students and educators.
-# Download and install PyMOL.
+<ol>
-# Enter command "fetch 1pgb".
+<li> Download and install PyMOL.
-# Menu: All, Action, remove waters.
+<li> Enter command "fetch 1pgb".
-# Menu: 1pgb, Action, generate, vacuum electrostatics, protein contact potential (local).
+<ul>
-# Enter command "bg_color white".
+<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!).