Jmol/Electrostatic potential: Difference between revisions
No edit summary |
No edit summary |
||
| (10 intermediate revisions by the same user not shown) | |||
| Line 30: | Line 30: | ||
https://pinostriccoli.altervista.org/le-superfici-molecolari-elettrostatiche-mep/ | https://pinostriccoli.altervista.org/le-superfici-molecolari-elettrostatiche-mep/ | ||
molcalc.org, e.g. http://molcalc.org/calculation/cc11a07f2bb4579391c1e0603665f673#/solvation | |||
Some theory on the Poisson Boltzmann equation: DOI:10.1002/jmr.577 | |||
<StructureSection load='1F36' size='340' side='right' caption='' scene=''> | |||
===Example 1: water=== | ===Example 1: water=== | ||
Electrostatic potential of <scene name='86/864093/Water/1'>water</scene> based on partial charges calculated in molcalc.org. | |||
Use this checkbox to toggle the potential on and off: | |||
<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked> | |||
<scriptWhenchecked>select all; isosurface molecular map mep; color isosurface range -0.05 0.05; color isosurface translucent | |||
</scriptWhenchecked> | |||
<checked>false</checked> | |||
<text>potential map</text> | |||
</jmolCheckbox> | |||
</jmol> | |||
After loading the .smol file, the following command was used to show the potential: | |||
<nowiki>isosurface molecular map mep color translucent</nowiki> | |||
===Example 2: the DNA-binding protein FIS=== | ===Example 2: the DNA-binding protein FIS=== | ||
DNA-binding (and DNA-bending) of <scene name='86/864093/Fis/1'>FIS</scene> is believed to be mostly electrostatic, explaining the low sequence-specificity and the high sensitive of interactions to ionic strength of the solvent. | |||
Use this checkbox to toggle the potential on and off: | |||
<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked> | |||
<scriptWhenchecked>select all; isosurface JVXL "http://proteopedia.org/wiki/images/2/2c/1F36.jvxl"</scriptWhenchecked> | |||
<checked>false</checked> | |||
<text>potential map</text> | |||
</jmolCheckbox> | |||
</jmol> | |||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||