View source for Mouse Manual

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{{Lang:Mouse_Manual}}
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== Manual for manipulating the molecules using the mouse in Jmol (also called 'mouse gestures') ==

Notes:
# In the usual configuration, "main button" is the left button, and "secondary button" is the right button.
# Reportedly, on single-button mice '''Alt   drag''' may be equivalent to '''drag with middle button'''.
<hr /><br />

<table border="1" cellspacing="0" width="100%">

<tr bgcolor="yellow" align="center">
 <td></td>
 <td>'''main button'''</td>
 <td>'''middle button'''</td>
 <td>'''secondary button'''</td>
</tr>
<tr bgcolor="yellow" align="center">
 <td></td>
 <td>(left)</td>
 <td>(middle)</td>
 <td>(right)</td>
</tr>
<tr>
 <td colspan="4"></td>
</tr>
<tr>
 <td>'''Open Jmol menu'''</td>
 <td>Ctrl + click<br />or click on 'Jmol' logo</td>
 <td></td>
 <td>click</td>
</tr>
<tr>
 <td colspan="4"></td>
</tr>
<tr>
 <td>'''Rotate around X,Y'''</td>
 <td>drag</td>
 <td></td>
 <td></td>
</tr>
<tr>
 <td colspan="4"></td>
</tr>
<tr>
 <td>'''Move along X,Y (= translate)'''</td>
 <td>Shift + double-click and drag</td>
 <td>double-click and drag</td>
 <td>Ctrl + drag</td>
</tr>
<tr>
 <td></td>
 <td colspan="3" align="center">''works both when clicking on the molecule or away from it''</td>
</tr>
<tr>
 <td colspan="4"></td>
</tr>
<tr>
 <td>'''Reset and centre'''</td>
 <td>Shift + double-click*</td>
 <td>double-click*</td>
 <td></td>
</tr>
<tr>
 <td></td>
 <td colspan="3" align="center">''*only works if double-click is done away from the molecule''</td>
</tr>
<tr>
 <td colspan="4">
</tr>
<tr>
 <td>'''Rotate around Z'''</td>
 <td>Shift + drag horizontally</td>
 <td>drag horizontally</td>
 <td>Shift + drag horizontally<br />(possibly fails in Mac's)</td>
</tr>
<tr>
 <td colspan="4"></td>
</tr>
<tr>
 <td>'''Zoom in / out'''</td>
 <td>Shift + drag vertically</td>
 <td>drag vertically</td>
 <td></td>
</tr>
<tr>
 <td></td>
 <td colspan="3" align="center">or use mouse wheel</td>
</tr>
<tr>
 <td colspan="4"></td>
</tr>
<tr>
 <td></td>
 <td colspan="3" align="center">''Implemented only on Jmol 10.00.22 prerelease and later:<br />Only work after a <tt>slab on</tt> command has been issued''</td>
</tr>
<tr>
 <td>'''Slab''' (slab from front)</td>
 <td>Ctrl+Shift + drag (vertically) *</td>
 <td></td>
 <td></td>
</tr>
<tr>
 <td>'''Depth''' (slab from back)</td>
 <td>Ctrl+Shift + double-click and drag (vertically) *</td>
 <td></td>
 <td></td>
</tr>
<tr>
 <td>'''Shift the slab''' (change slab and depth maintaining constant thickness)</td>
 <td>Alt+Ctrl+Shift + drag (vertically) *</td>
 <td></td>
 <td></td>
</tr>
<tr>
 <td></td>
 <td colspan="3" align="center">''*if this fails on a Mac, try pressing the mouse button first, then the Ctrl Shift keys, then drag''</td>
</tr>
<tr>
 <td></td>
 <td colspan="3" align="center">''Slab can be tested in [http://biomodel.uah.es/Jmol/slab/ this page]''</td>
</tr>
</table>

<br /><br />
== How to select ==

* Use the appropriate picking command, e.g.

'''set picking group'''

: to toggle selection for an entire amino acid by clicking on one of its atoms,
* Click on an atom will toggle selection status.
* Most useful while

'''set display selected'''

: is set to monitor the selection status.

<br />

To toggle the selection status of individula atoms:<br>
Using the menus:
<ol>
<li>Jmol->Main Menu->Select->Selection Halos (This is optional but very helpful. It shows you which atoms are selected by plaing a golden ring around it.)
<li>Jmol->Main Menu->Select->None (Needed because "select all" is the default at load time. Notice the non-zero number in parenthesis after the word select in the main menu. That is the number of items currently selected.
<li>Jmol->Main Menu->Set picking->Select Atom
</ol>
Now click an atom once to select, click again to deselect.
The halos let me know the current selection state of each atom
and the count in parenthesis after the Select in Jmol->Main Menu
gives me a count of the number of atoms selected.

== How to make measurements ==

* Distance (2 atoms):
*# double-click on the starting atom
*# to fix a distance measurement, double-click on second atom
* Angle (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 (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