Jmol/Application: Difference between revisions

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* ~~'''Load your molecule.'''~~ There are several ways to load a [[PDB file]]:

==Loading a Molecule==

*There are several ways to load a [[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). There must be a space between "load" and "=", and no space between "=" and the PDB ID. The "=" tells Jmol to get the file from the [[Protein Data Bank]]. Substitute your [[PDB code]] for 1d66.

**If you have downloaded the PDB file:

***Drag the file and drop it into the black Jmol window.

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***Open Jmol's ''File'' menu (above the black window), and Open or Open Recent.

* 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.

==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==

Jmol/Application: Difference between revisions

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@@ Line 5: / Line 5: @@
 {{Template:Jmol_application_instructions}}
-* '''Load your molecule.''' There are several ways to load a [[PDB file]]:
+==Loading a Molecule==
+*There are several ways to load a [[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). There must be a space between "load" and "=", and no space between "=" and the PDB ID. The "=" tells Jmol to get the file from the [[Protein Data Bank]]. Substitute your [[PDB code]] for 1d66.
 **If you have downloaded the PDB file:
 ***Drag the file and drop it into the black Jmol window.
@@ Line 13: / Line 15: @@
 ***Open Jmol's ''File'' menu (above the black window), and Open or Open Recent.
-* 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.
+==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==