Jmol Help: Difference between revisions
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</tr> | </tr> | ||
</table> | </table> | ||
== Jmol measurements == | |||
* Distance between 2 atoms: | |||
# double-click on the starting atom | |||
# to fix a distance measurement, double-click on second atom | |||
* Angle between 3 atoms: | |||
# double-click on the starting atom | |||
# click on the second atom (central atom in angle) | |||
# to fix an angle measurement, double-click on third atom | |||
* Torsion angle or dihedral between 4 atoms: | |||
# double-click on the starting atom | |||
# click on the second atom | |||
# click on the third atom</p> | |||
# to fix a dihedral angle measurement, double-click on fourth atom | |||
* In all cases: | |||
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement | |||
** move outside the window in order to cancel the measurement | |||
** make the same measurement again in order to delete the measurement | |||
== Jmol default colours == | == Jmol default colours == | ||
=== Elements === | === Elements: CPK colour scheme === | ||
Hover over any element to see more information (Atomic Number, Symbol, Element Name) | Hover over any element to see more information (Atomic Number, Symbol, Element Name) | ||
<table style="text-align:center"> | <table style="text-align:center"> | ||
<tr> | <tr> | ||
<td title="1 H Hydrogen" style="background-color:# | <th title="Group1, the alkali metals" style="width: 2em">1</th> | ||
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th> | |||
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th> | |||
<th title="Group4, the titanium group" style="width: 2em">4</th> | |||
<th title="Group5, the vanadium group" style="width: 2em">5</th> | |||
<th title="Group6, the chromium group" style="width: 2em">6</th> | |||
<th title="Group7, the manganese group" style="width: 2em">7</th> | |||
<th title="Group8, the iron group" style="width: 2em">8</th> | |||
<th title="Group9, the cobalt group" style="width: 2em">9</th> | |||
<th title="Group10, the nickel group" style="width: 2em">10</th> | |||
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th> | |||
<th title="Group12, the zinc group" style="width: 2em">12</th> | |||
<th title="Group13, the boron group" style="width: 2em">13</th> | |||
<th title="Group14, the carbon group" style="width: 2em">14</th> | |||
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th> | |||
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th> | |||
<th title="Group17, the halogens" style="width: 2em">17</th> | |||
<th title="Group18, the noble gases" style="width: 2em">18</th> | |||
</tr> | |||
<tr> | |||
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td> | |||
<td rowspan="1" colspan="16"></td> | <td rowspan="1" colspan="16"></td> | ||
<td title="2 He Helium" style="background-color:#d9ffff">He</td> | <td title="2 He Helium" style="background-color:#d9ffff">He</td> | ||
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<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td> | <td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td> | ||
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td> | <td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td> | ||
<td> | <td title="110 Ds Darmstadtium" bgcolor="#eb0026">Ds</td> | ||
<td> | <td title="111 Rg Roentgenium" bgcolor="#eb0026">Rg</td> | ||
<td> | <td title="112 Cn Copernicium" bgcolor="#eb0026">Cn</td> | ||
<td> </td> | <td> </td> | ||
<td> </td> | <td> </td> | ||
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</table> | </table> | ||
== Biological macromolecules == | === Biological macromolecules === | ||
=== Primary structure === | ==== Primary structure ==== | ||
==== Amino acid residues ==== | ===== Amino acid residues: Amino colour scheme ===== | ||
<table style="text-align: center;"> | <table style="text-align: center;"> | ||
<tr> | <tr> | ||
<td title="alanine" style="width: 2em; background-color: #8CFF8C | <td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala | ||
</td> | |||
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg | |||
</td> | |||
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn | |||
</td> | |||
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp | |||
</td> | |||
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys | |||
</td> | |||
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln | |||
</td> | |||
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu | |||
</td> | |||
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly | |||
</td> | |||
<td title="histidine" style="width: 2em; background-color: #8282D2"> His | |||
</td> | |||
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile | |||
</td> | |||
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu | |||
</td> | |||
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys | |||
</td> | |||
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met | |||
</td> | |||
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe | |||
</td> | |||
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro | |||
</td> | |||
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser | |||
</td> | |||
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr | |||
</td> | |||
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp | |||
</td> | |||
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr | |||
</td> | |||
<td title="valine" style="width: 2em; background-color: #0F820F"> Val | |||
</td> | |||
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx | |||
</td> | |||
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx | |||
</td> | |||
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx | |||
</td> | |||
</tr> | |||
</table> | |||
===== Amino acid residues: Shapely colour scheme ===== | |||
<table style="text-align: center;"> | |||
<tr> | |||
<tr> | |||
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala | |||
</td> | </td> | ||
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg | <td title="arginine" style="width: 2em; background-color: #00007C;"> Arg | ||
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<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp | <td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp | ||
</td> | </td> | ||
<td title="cystine" style="width: 2em; background-color: # | <td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys | ||
</td> | </td> | ||
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln | <td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln | ||
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</td> | </td> | ||
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx | <td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx | ||
</td></tr></table> | </td> | ||
</tr> | |||
</table> | |||
===== Nucleotide base residues: Shapely colour scheme ===== | |||
<table> | <table> | ||
<tr> | <tr> | ||
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<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U | <td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U | ||
</td></tr></table> | </td></tr></table> | ||
=== Secondary structure === | |||
==== Polypeptides ==== | ==== Secondary structure ==== | ||
===== Polypeptides, nucleic acids and carbohydrates ===== | |||
<table> | <table> | ||
<tr> | <tr> | ||
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<td style="width:5em; background-color: #FFFFFF; text-align: center;"> | <td style="width:5em; background-color: #FFFFFF; text-align: center;"> | ||
</td> | </td> | ||
<td style="width:5em; background-color: #A6A6FA; text-align: center;"> | <td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate | ||
</td> | </td> | ||
<td style="width:5em; background-color: #808080; text-align: center;">other | <td style="width:5em; background-color: #808080; text-align: center;">other | ||
</td></tr></table> | </td> | ||
==== | </tr> | ||
= | </table> | ||
==== Polypeptides and nucleic acids ==== | |||
==== Tertiary structure ==== | |||
===== Polypeptides and nucleic acids ===== | |||
<table style="border-spacing:0;border-collapse:collapse"> | <table style="border-spacing:0;border-collapse:collapse"> | ||
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<td style="width:1em; background-color:#ff0000"> | <td style="width:1em; background-color:#ff0000"> | ||
</td></tr></table> | </td></tr></table> | ||
==More== | ==More== |
Latest revision as of 20:59, 30 March 2014
Help with using the Jmol_filter
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Click | |
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Reset & centre | Shift + double-click (away from molecule) | Double-click (away from molecule) | |
Resize Jmol | Click & drag bottom-right corner |
Jmol measurements
- Distance between 2 atoms:
- double-click on the starting atom
- to fix a distance measurement, double-click on second atom
- Angle between 3 atoms:
- double-click on the starting atom
- click on the second atom (central atom in angle)
- to fix an angle measurement, double-click on third atom
- Torsion angle or dihedral between 4 atoms:
- double-click on the starting atom
- click on the second atom
- click on the third atom
- to fix a dihedral angle measurement, double-click on fourth atom
- In all cases:
- move pointer over destination atom in order to see measurement results without leaving a permanent measurement
- move outside the window in order to cancel the measurement
- make the same measurement again in order to delete the measurement
Jmol default colours
Elements: CPK colour scheme
Hover over any element to see more information (Atomic Number, Symbol, Element Name)
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
H | He | ||||||||||||||||
Li | Be | B | C | N | O | F | Ne | ||||||||||
Na | Mg | Al | Si | P | S | Cl | Ar | ||||||||||
K | Ca | Sc | Ti | V | Cr | Mn | Fe | Co | Ni | Cu | Zn | Ga | Ge | As | Se | Br | Kr |
Rb | Sr | Y | Zr | Nb | Mo | Tc | Ru | Rh | Pd | Ag | Cd | In | Sn | Sb | Te | I | Xe |
Cs | Ba | * | Hf | Ta | W | Re | Os | Ir | Pt | Au | Hg | Tl | Pb | Bi | Po | At | Rn |
Fr | Ra | ** | Rf | Db | Sg | Bh | Hs | Mt | Ds | Rg | Cn | ||||||
* | La | Ce | Pr | Nd | Pm | Sm | Eu | Gd | Tb | Dy | Ho | Er | Tm | Yb | Lu | ||
** | Ac | Th | Pa | U | Np | Pu | Am | Cm | Bk | Cf | Es | Fm | Md | No | Lr |
Biological macromolecules
Primary structure
Amino acid residues: Amino colour scheme
Ala | Arg | Asn | Asp | Cys | Gln | Glu | Gly | His | Ile | Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val | Asx | Glx | Xxx |
Amino acid residues: Shapely colour scheme
Ala | Arg | Asn | Asp | Cys | Gln | Glu | Gly | His | Ile | Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val | Asx | Glx | Xxx |
Nucleotide base residues: Shapely colour scheme
A | G | I | C | T | U |
Secondary structure
Polypeptides, nucleic acids and carbohydrates
α helix | 310 helix | π helix | β strand | (β) turn | other | DNA | RNA | other | carbohydrate | other |
Tertiary structure
Polypeptides and nucleic acids
N-terminal or 5’- | C-terminal or 3’- | |||||||||||||||||||||||||||||||
More
For further information see: