Difference between revisions of "Mouse Manual"

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m (Reverted edits by Tania (talk) to last revision by AngelHerraez)
Line 171: Line 171:
 
** move outside the window in order to cancel the measurement
 
** move outside the window in order to cancel the measurement
 
** make the same measurement again in order to delete the measurement
 
** make the same measurement again in order to delete the measurement
 +
 +
== How to change atom coordinates ==
 +
This section describes how to move individual atoms within a model
 +
with the mouse.
 +
 +
Transformations like rotations or translations are normally applied to all atoms identically. And the stored coordinates of the
 +
atoms are not changed. But Jmol can also be configured to move some
 +
atoms individually and store the changed coordinates permanently.
 +
 +
There are two modes available:
 +
# Moving only whole molecules, e.g. a whole chain
 +
# Moving atoms independent of their connectivity
 +
 +
This section concentrates on the second mode. The two following
 +
settings are needed to activate it:
 +
# [http://chemapps.stolaf.edu/jmol/docs/#k969 set allowMoveAtoms] on;
 +
# [http://chemapps.stolaf.edu/jmol/docs/#k971 set allowRotateSelected] on;
 +
 +
There are additional switches available that influence what can be
 +
done and how it can be done:
 +
# [http://chemapps.stolaf.edu/jmol/docs/#setpicking set picking]
 +
# [http://chemapps.stolaf.edu/jmol/docs/#setpickingstyle set pickingStyle]
 +
# [http://chemapps.stolaf.edu/jmol/docs/#k993 set dragSelected]
 +
 +
The table below summarizes information for three of the possible
 +
setting combinations (tested in Jmol 14.3.13).
 +
 +
<table style="margin-left: 1.2em; margin-top: 0.8em;">
 +
    <tr>
 +
      <th></th>
 +
      <th colspan="9" style="background-color: rgb(245,235,210); text-align: left; padding:0.4em;">Basic options:
 +
<ul style="margin: 0.5em;">
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#k969 set allowMoveAtoms] on;</li>
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#k971 set allowRotateSelected] on;</li>
 +
</ul>
 +
      </th>
 +
    </tr>
 +
    <tr>
 +
      <th></th>
 +
      <th colspan="3" style="background-color: rgb(240,240,240); text-align: left; padding:0.4em;">Option Set 1:
 +
<ul style="margin: 0.5em;">
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#setpicking set picking] dragSelected;</li>
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#setpickingstyle set pickingStyle] select toggle;</li>
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#k993 set dragSelected] off;</li>
 +
</ul>
 +
      </th>
 +
      <th colspan="3" style="background-color: rgb(220,200,190); text-align: left; padding:0.4em;">Option Set 2:
 +
<ul style="margin: 0.5em;">
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#setpicking set picking] dragSelected;</li>
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#setpickingstyle set pickingStyle] select drag;</li>
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#k993 set dragSelected] off;</li>
 +
</ul>
 +
      </th>
 +
      <th colspan="3" style="background-color: rgb(180,245,220); text-align: left; padding:0.4em;">Option Set 3:
 +
<ul style="margin: 0.5em;">
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#setpicking set picking] atom;</li>
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#setpickingstyle set pickingStyle] select toggle;</li>
 +
  <li>[http://chemapps.stolaf.edu/jmol/docs/#k993 set dragSelected] on;</li>
 +
</ul>
 +
      </th>
 +
    </tr>
 +
    <tr>
 +
      <th></th>
 +
      <th style="background-color: rgb(220,220,220); text-align: left; padding: 0.4em;">Click Type</th>
 +
      <th style="background-color: rgb(220,220,220); text-align: left; padding: 0.4em;">Click Target</th>
 +
      <th style="background-color: rgb(220,220,220); text-align: left; padding: 0.4em;">Comment</th>
 +
      <th style="background-color: rgb(200,185,175); text-align: left; padding: 0.4em;">Click Type</th>
 +
      <th style="background-color: rgb(200,185,175); text-align: left; padding: 0.4em;">Click Target</th>
 +
      <th style="background-color: rgb(200,185,175); text-align: left; padding: 0.4em;">Comment</th>
 +
      <th style="background-color: rgb(170,230,205); text-align: left; padding: 0.4em;">Click Type</th>
 +
      <th style="background-color: rgb(170,230,205); text-align: left; padding: 0.4em;">Click Target</th>
 +
      <th style="background-color: rgb(170,230,205); text-align: left; padding: 0.4em;">Comment</th>
 +
 +
    <tr>
 +
      <th colspan="10" style="background-color: rgb(220,230,180);
 +
  text-align: left; padding:0.4em;">Atom Movement (only selected atoms)</th>
 +
    </tr>
 +
    <tr>
 +
      <th  style="background-color: rgb(235,245,190); text-align: left; padding:0.4em;">x/y-shift<br>(along screen axes)</th>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;">drag</td>
 +
      <td style="background-color: rgb(240,240,240); padding:
 +
  0.4em;">any atom</td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">drag</td>
 +
      <td style="background-color: rgb(220,200,190); padding:
 +
  0.4em;">any atom</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">shift-alt-drag</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">anywhere</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
    </tr>
 +
    <tr>
 +
      <th  style="background-color: rgb(235,245,190); text-align: left; padding:0.4em;">z-shift<br>(perpendicular to screen)</th>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;">shift-drag</td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;">any atom</td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">not available</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">not available</td>
 +
    </tr>
 +
    <tr>
 +
      <th  style="background-color: rgb(235,245,190); text-align: left; padding:0.4em;">rotate</th>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;">alt-drag</td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;">any atom</td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">not available</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">alt-drag</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">anywhere</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
    </tr>
 +
    <tr>
 +
      <th colspan="10" style="background-color: rgb(220,230,180);
 +
  text-align: left; padding:0.4em;">Atom Selection</th>
 +
    </tr>
 +
    <tr>
 +
      <th rowspan="2" style="background-color: rgb(235,245,190); text-align: left; padding:0.4em;">select a single atom</th>
 +
      <td rowspan="2" style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td rowspan="2" style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td rowspan="2" style="background-color: rgb(240,240,240); padding: 0.4em;">not available</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">shift-drag</td>
 +
      <td style="background-color: rgb(220,200,190); padding:
 +
  0.4em;">around an unselected atom</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">click</td>
 +
      <td style="background-color: rgb(180,245,220); padding:
 +
  0.4em;">an unselected atom</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
    </tr>
 +
 +
    <tr>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">alt-drag</td>
 +
      <td style="background-color: rgb(220,200,190); padding:
 +
  0.4em;">around an atom</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">double-click</td>
 +
      <td style="background-color: rgb(180,245,220); padding:
 +
  0.4em;">an atom</td>
 +
      <td style="background-color: rgb(180,245,220); padding:
 +
      0.4em;">other atoms are deselected</td>
 +
    </tr>
 +
    <tr>
 +
      <th  style="background-color: rgb(235,245,190); text-align: left; padding:0.4em;">deselect a single atom</th>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;">not available</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">shift-drag</td>
 +
      <td style="background-color: rgb(220,200,190); padding:
 +
  0.4em;">around a selected atom</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">click</td>
 +
      <td style="background-color: rgb(180,245,220); padding:
 +
  0.4em;">a selected atom</td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
    </tr>
 +
    <tr>
 +
      <th  rowspan="2" style="background-color: rgb(235,245,190); text-align: left; padding:0.4em;">select multiple atoms</th>
 +
      <td rowspan="2" style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td rowspan="2" style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td rowspan="2" style="background-color: rgb(240,240,240); padding: 0.4em;">not available</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">shift-drag</td>
 +
      <td style="background-color: rgb(220,200,190); padding:
 +
  0.4em;">around unselected atoms</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td rowspan="2" style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
      <td rowspan="2" style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
      <td rowspan="2" style="background-color: rgb(180,245,220); padding: 0.4em;">not available</td>
 +
    </tr>
 +
 +
    <tr>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">alt-drag</td>
 +
      <td style="background-color: rgb(220,200,190); padding:
 +
  0.4em;">around atoms</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
    </tr>
 +
 +
    <tr>
 +
      <th  style="background-color: rgb(235,245,190); text-align: left; padding:0.4em;">deselect multiple atoms</th>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(240,240,240); padding: 0.4em;">not available</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;">shift-drag</td>
 +
      <td style="background-color: rgb(220,200,190); padding:
 +
  0.4em;">around selected atoms</td>
 +
      <td style="background-color: rgb(220,200,190); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;"></td>
 +
      <td style="background-color: rgb(180,245,220); padding: 0.4em;">not available</td>
 +
    </tr>
 +
    <tr>
 +
      <th colspan="10" style="background-color: rgb(220,230,180);
 +
  text-align: left; padding:0.4em;">Summary</th>
 +
    </tr>
 +
    <tr>
 +
      <th></th>
 +
      <td colspan="3" style="background-color: rgb(240,240,240); text-align: left; padding:0.4em;">
 +
Option set 1 (+ basic options) totally disables mouse-based selection changes and enables all
 +
three movement types (x/y-shift, z-shift, rotate).
 +
      </td>
 +
      <td colspan="3" style="background-color: rgb(220,200,190); text-align: left; padding:0.4em;">
 +
Option set 2 (+ basic options) enables mouse-based single/multiple atom selection changes and
 +
enables only one movement type (x/y-shift).
 +
      </td>
 +
      <td colspan="3" style="background-color: rgb(180,245,220); text-align: left; padding:0.4em;">
 +
Option set 3 (+ basic options) enables mouse-based single atom selection changes and enables two
 +
movement types (x/y-shift, rotate).
 +
      </td>
 +
    </tr>
 +
</table>

Revision as of 09:29, 27 April 2015

Jmol / JSmol Tutorials

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Reference: English – Other: Español · Français · 日本語 ·


Manual for manipulating the molecules using the mouse in Jmol (also called 'mouse gestures')

Notes:

  1. In the usual configuration, "main button" is the left button, and "secondary button" is the right button.
  2. Reportedly, on single-button mice Alt drag may be equivalent to drag with middle button.


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



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.


To toggle the selection status of individula atoms:
Using the menus:

  1. 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.)
  2. 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.
  3. Jmol->Main Menu->Set picking->Select Atom

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):
    1. double-click on the starting atom
    2. to fix a distance measurement, double-click on second atom
  • Angle (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 (4 atoms)
    1. double-click on the starting atom
    2. click on the second atom
    3. click on the third atom
    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

How to change atom coordinates

This section describes how to move individual atoms within a model with the mouse.

Transformations like rotations or translations are normally applied to all atoms identically. And the stored coordinates of the atoms are not changed. But Jmol can also be configured to move some atoms individually and store the changed coordinates permanently.

There are two modes available:

  1. Moving only whole molecules, e.g. a whole chain
  2. Moving atoms independent of their connectivity

This section concentrates on the second mode. The two following settings are needed to activate it:

  1. set allowMoveAtoms on;
  2. set allowRotateSelected on;

There are additional switches available that influence what can be done and how it can be done:

  1. set picking
  2. set pickingStyle
  3. set dragSelected

The table below summarizes information for three of the possible setting combinations (tested in Jmol 14.3.13).

Basic options:
Option Set 1: Option Set 2: Option Set 3:
Click Type Click Target Comment Click Type Click Target Comment Click Type Click Target Comment
Atom Movement (only selected atoms)
x/y-shift
(along screen axes)
drag any atom drag any atom shift-alt-drag anywhere
z-shift
(perpendicular to screen)
shift-drag any atom not available not available
rotate alt-drag any atom not available alt-drag anywhere
Atom Selection
select a single atom not available shift-drag around an unselected atom click an unselected atom
alt-drag around an atom double-click an atom other atoms are deselected
deselect a single atom not available shift-drag around a selected atom click a selected atom
select multiple atoms not available shift-drag around unselected atoms not available
alt-drag around atoms
deselect multiple atoms not available shift-drag around selected atoms not available
Summary

Option set 1 (+ basic options) totally disables mouse-based selection changes and enables all three movement types (x/y-shift, z-shift, rotate).

Option set 2 (+ basic options) enables mouse-based single/multiple atom selection changes and enables only one movement type (x/y-shift).

Option set 3 (+ basic options) enables mouse-based single atom selection changes and enables two movement types (x/y-shift, rotate).