Jmol Help: Difference between revisions
From MoodleDocs
Line 59: | Line 59: | ||
<table style="text-align:center"> | <table style="text-align:center"> | ||
<tr> | <tr> | ||
<th title="Group1, the alkali metals">1</th> | <th title="Group1, the alkali metals" style="width: 2em">1</th> | ||
<th title="Group2, the alkaline earth metals">2</th> | <th title="Group2, the alkaline earth metals" style="width: 2em">2</th> | ||
<th title="Group3, the scandium group including the lanthanoids and actinoids">3</th> | <th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th> | ||
<th title="Group4, the titanium group ">4</th> | <th title="Group4, the titanium group" style="width: 2em">4</th> | ||
<th title="Group5, the vanadium group ">5</th> | <th title="Group5, the vanadium group" style="width: 2em">5</th> | ||
<th title="Group6, the chromium group ">6</th> | <th title="Group6, the chromium group" style="width: 2em">6</th> | ||
<th title="Group7, the manganese group ">7</th> | <th title="Group7, the manganese group" style="width: 2em">7</th> | ||
<th title="Group8, the iron group ">8</th> | <th title="Group8, the iron group" style="width: 2em">8</th> | ||
<th title="Group9, the cobalt group ">9</th> | <th title="Group9, the cobalt group" style="width: 2em">9</th> | ||
<th title="Group10, the nickel group ">10</th> | <th title="Group10, the nickel group" style="width: 2em">10</th> | ||
<th title="Group11, the copper group, coinage metals ">11</th> | <th title="Group11, the copper group, coinage metals" style="width: 2em">11</th> | ||
<th title="Group12, the zinc group ">12</th> | <th title="Group12, the zinc group" style="width: 2em">12</th> | ||
<th title="Group13, the boron group">13</th> | <th title="Group13, the boron group" style="width: 2em">13</th> | ||
<th title="Group14, the carbon group">14</th> | <th title="Group14, the carbon group" style="width: 2em">14</th> | ||
<th title="Group15, the pnictogens, nitrogen group">15</th> | <th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th> | ||
<th title="Group16, the chalcogens, oxygen group">16</th> | <th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th> | ||
<th title="Group17, the halogens">17</th> | <th title="Group17, the halogens" style="width: 2em">17</th> | ||
<th title="Group18, the noble gases">18</th> | <th title="Group18, the noble gases" style="width: 2em">18</th> | ||
</tr> | </tr> | ||
<tr> | <tr> |
Revision as of 19:56, 30 March 2014
Help with using the Jmol_filter
Jmol mouse control
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.
Action | Main (left) button | Middle button | Secondary (right) button |
---|---|---|---|
Jmol menu | Click on Jmol logo or Ctrl + click |
Click | |
Rotate X,Y | Click & drag | ||
Translate X,Y | Shift + double-click & drag | Double-click & drag | Ctrl + click & drag |
Rotate Z | Shift + click & drag horizontally | Click & drag horizontally | Shift + click & drag horizontally |
Zoom | Shift + click & drag vertically | Click & drag vertically or mouse wheel |
|
Reset & centre | Shift + double-click (away from molecule) | Double-click (away from molecule) | |
Resize Jmol | Click & drag bottom-right corner |
Jmol default colours
Elements
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 | |||||||||
* | 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
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
A | G | I | C | T | U |
Secondary structure
Polypeptides | Nucleic acids | |||||||||||
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’- | |||||||||||||||||||||||||||||||
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
More
For further information see: