X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;fp=help%2Fhtml%2Ffeatures%2Fjmol.html;h=e7f963b5ef213cf9c4ab6c911eb246fa28ab325e;hb=c53aeee9a688f68d64106a968876e542f701fbc6;hp=66edaf9c3e5243d224a5ac331ba517768e2ebf4e;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see
The Jmol PDB Viewer +
The interactive structure viewing window is opened by selecting +the "Sequence→View PDB entry:" entry in +the sequence id pop-up menu. This +can only be done for sequences which have an associated +PDB structure. +
Since Jalview 2.3, Jmol +has been integrated into Jalview. It is automatically used by the +application, and should also run in the applet in all latest web +browsers. If jmol is not available, then the original internal pdb viewer will be used as a fallback. +
+Controls
+The structure is by default rendered as a ribbon diagram. Moving the +mouse over the structure brings up tooltips giving the residue name, +PDB residue number and chain code, atom name and number +([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue +in any associated sequences, then this will be highlighted in each +one's alignment window. The converse also occurs - moving the mouse +over an associated residue in an alignment window highlights the associated +atoms in the displayed structures.
+Selecting a residue highlights its associated sequence residue +and alpha carbon location. Double clicking an atom allows distances to +be measured from it to any other atom in the structure.
++
Action | +Windows | +Unix | +Mac/OSX | +
Rotate View | +Left Click and Drag | +Left Click and Drag | +Click and Drag | +
Zoom | +Shift + Left Click drag mouse up or down |
+ Shift + Left Click or middle button drag + mouse up or down |
+ Left-Alt + Click and drag mouse up or down | +
Select/ + Deselect + Residue |
+ Left Click | +Left Click | +Click | +
Roll View | +Shift + Left Click drag mouse to left or + right |
+ Shift + Left Click or middle button drag mouse to left or right |
+ Left-Alt + Click and drag mouse to left or right | +
Move Origin | +Shift+Control+Left Click or Middle Button + + Drag |
+ Middle-Button and drag |
+ Shift+Control+Left Click or Middle Button + and drag |
+
Jmol Menu | +Right-Click | +Right-Click | +Apple-Click | +
The window has four menus: +
Functionality provided by Jmol +
The Jmol menu provides access to a number of features for +controlling the colour and display of molecules, adding measurements and +labels, plotting surfaces, and display animation. The 'Set Picking' +menu controls the behaviour of single and double mouse clicking on the +structure.
+The state of each Jmol display is stored within jalview archives as a jmol state recovery script +file. This means that any Jmol visualization effects that +you add beyond those provided by Jalview will be able to be stored and +recovered along with the displayed alignments in Jalview. +
More Information +
Jmol is a sophisticated program in its own right, with its own +command console and scripting language. Only the essentials have been +described here - the interested reader is referred to +Jmol's own comprehensive +online documenation.
+ +