Jmol/Application: Difference between revisions
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Pages in Proteopedia use | Pages in Proteopedia use a javascript form of [[Jmol]] called JSmol, which operates automatically within a web browser. No installation or setup is needed. For some advanced projects, you may wish to use the Jmol standalone '''application''' (no web browser involved once it is downloaded). Here are instructions: | ||
* The Jmol application requires Java (free) in order to run. You can download and install it easily at [http://java.com Java.com]. | |||
{{Template:Jmol_application_instructions}} | {{Template:Jmol_application_instructions}} | ||
* | ==Loading a Molecule== | ||
*There are several ways to load a [[PDB file]]: | |||
**If you do not have a downloaded copy of the PDB file: | **If you do not have a downloaded copy of the PDB file: | ||
***Enter the command "load =1d66" in the white window (without typing the quotation marks). The "=" tells Jmol to get the file from the [[Protein Data Bank]]. Substitute your [[PDB code]] for 1d66. | ***Enter the command "load =1d66" in the white window (without typing the quotation marks). The "=" tells Jmol to get the file from the [[Protein Data Bank]]. Substitute your [[PDB code]] for 1d66. | ||
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***Enter the command "load ?", and a file picking dialog will appear. | ***Enter the command "load ?", and a file picking dialog will appear. | ||
***Open Jmol's ''File'' menu (above the black window), and Open or Open Recent. | ***Open Jmol's ''File'' menu (above the black window), and Open or Open Recent. | ||
==Commands and Script Files== | |||
You are now ready to '''enter Jmol commands''' into the Jmol Script Console. It is usually convenient to gather commands in script files. '''Command script files''' must be edited with a [[Help:Plain text editors|plain text editor]]. The names of command script files should always end '''.spt'''. You can run a script file by dragging it and dropping it into the molecular graphics window of Jmol. | |||
==See Also== | ==See Also== | ||
* [[Jmol]] | * [[Jmol]] | ||
* [[Jmol/Visualizing large molecules]] | * [[Jmol/Visualizing large molecules]] | ||
* [http://www.proteopedia.org/wiki/index.php/Special:PrefixIndex/Jmol Pages about Jmol-specific topics] | * [http://www.proteopedia.org/wiki/index.php/Special:PrefixIndex/Jmol Pages about Jmol-specific topics] (This link runs a search for all pages within Proteopedia that have titles beginning with "Jmol".) | ||
* [[Scene authoring tools]] | * [[Scene authoring tools]] | ||