Difference between revisions of "Jmol Help"

Jump to: navigation, search
(Elements)
(Jmol measurements)
 
(2 intermediate revisions by the same user not shown)
Line 53: Line 53:
 
     </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 ==
Line 175: Line 196:
 
       <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>&nbsp;</td>
+
       <td title="110 Ds Darmstadtium" bgcolor="#eb0026">Ds</td>
       <td>&nbsp;</td>
+
       <td title="111 Rg Roentgenium" bgcolor="#eb0026">Rg</td>
       <td>&nbsp;</td>
+
       <td title="112 Cn Copernicium" bgcolor="#eb0026">Cn</td>
 
       <td>&nbsp;</td>
 
       <td>&nbsp;</td>
 
       <td>&nbsp;</td>
 
       <td>&nbsp;</td>
Line 463: Line 484:
 
<td style="width:1em; background-color:#ff0000">
 
<td style="width:1em; background-color:#ff0000">
 
</td></tr></table>
 
</td></tr></table>
 
== Jmol measurements ==
 
* Distance between 2 atoms:
 
# double-click on the starting atom
 
# to fix a distance measurement, double-click on second atom</p>
 
   
 
* 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</p>
 
 
* 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
 
  
 
==More==
 
==More==

Latest revision as of 20:59, 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 measurements

  • Distance between 2 atoms:
  1. double-click on the starting atom
  2. to fix a distance measurement, double-click on second atom
  • Angle between 3 atoms:
  1. double-click on the starting atom
  2. click on the second atom (central atom in angle)
  3. to fix an angle measurement, double-click on third atom
  • Torsion angle or dihedral between 4 atoms:
  1. double-click on the starting atom
  2. click on the second atom
  3. click on the third atom</p>
  4. 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:

Jmol

Jmol Wiki

Jmol Scripting Reference