Template:Jmol application instructions: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 2: | Line 2: | ||
* '''Free java memory''' if your project involves large molecules or assemblies. This is not necessary if your molecule(s) are modest in size (up to ~30,000 atoms). If you skip this step and Jmol gives you an "Out Of Memory" error, then come back and do this step. Close any java-based programs. Close all browser windows or tabs that contain the Jmol applet. Close the Jmol application. You can check Jmol's java memory usage by clicking on ''Jmol'' (in either the applet or the application), then on the main menu, About, System. | * '''Free java memory''' if your project involves large molecules or assemblies. This is not necessary if your molecule(s) are modest in size (up to ~30,000 atoms). If you skip this step and Jmol gives you an "Out Of Memory" error, then come back and do this step. Close any java-based programs. Close all browser windows or tabs that contain the Jmol applet. Close the Jmol application. You can check Jmol's java memory usage by clicking on ''Jmol'' (in either the applet or the application), then on the main menu, About, System. | ||
**Alternatively, or if you still get an ''Out Of Memory'' error, you can [http://wiki.jmol.org/index.php/Jmol_Application#Giving_Jmol_more_memory_to_work_with give Jmol more memory to work with]. | |||
*'''Run the Jmol application''': Double-click Jmol.jar in your working folder, and a black window will appear titled "Jmol". If the white "Jmol Script Console" window does not appear, use Jmol's File menu (at the top), Console to open it. Now you are ready to enter commands (see the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Interactive Scripting Manual]). | *'''Run the Jmol application''': Double-click Jmol.jar in your working folder, and a black window will appear titled "Jmol". If the white "Jmol Script Console" window does not appear, use Jmol's File menu (at the top), Console to open it. Now you are ready to enter commands (see the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Interactive Scripting Manual]). | ||
*'''Copying and pasting:''' To copy or paste commands in the white Jmol Script Console window, use <font color="red">'''Ctrl-C'''</font> and <font color="red">'''Ctrl-V'''</font>, '''even if working on an Apple Mac OS X!'''. In java windows, the usual Apple Cmd-C and Cmd-V don't work! You can also select blocks of text with your mouse, then drag and drop them. | *'''Copying and pasting:''' To copy or paste commands in the white Jmol Script Console window, use <font color="red">'''Ctrl-C'''</font> and <font color="red">'''Ctrl-V'''</font>, '''even if working on an Apple Mac OS X!'''. In java windows, the usual Apple Cmd-C and Cmd-V don't work! You can also select blocks of text with your mouse, then drag and drop them. | ||
