Molecular Playground/Procedures: Difference between revisions
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Eric Martz (talk | contribs) →Installing a state script from Proteopedia: adding content |
Eric Martz (talk | contribs) →Installing a state script from Proteopedia: adding content |
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'''Display the state script: ''' Display your scene in Proteopedia. Toggle spinning OFF. Orient the molecule as you would like it to first appear, by rotating it with the mouse. Click on "Jmol" (or right click) to open Jmol's menu, and select Show, Current state. | '''Display the state script: ''' Display your scene in Proteopedia. Toggle spinning OFF. Orient the molecule as you would like it to first appear, by rotating it with the mouse. Click on "Jmol" (or right click) to open Jmol's menu, and select Show, Current state. | ||
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'''Save the state script into a file:''' Block select the entire state script in the upper frame of the Jmol Script Console window. (On Macs, you'll have to use the mouse for this.) Copy the entire state script into a text editing program. On '''Macs''', you'll have to '''drag the blocked text and drop it''' into the text editor program. Save the state script into a file named e.g. yourMolecule_state.spt. The file type '''.spt''' signifies that this is a Jmol script. Be sure to save it as plain text. On Macs, plain text editors are TextEdit (comes with OS X; select ''Make Plain Text'' on the ''Format'' menu), and TextWrangler (free from [http://barebonessoftware.com BareBoneSoftware]). On Windows, you could use WordPad (select ''Text Document'' on the ''save as type'' menu), Notepad, or MS Word (select ''Plain Text'' on the ''save as type'' menu). | '''Save the state script into a file:''' Block select the entire state script in the upper frame of the Jmol Script Console window. (On Macs, you'll have to use the mouse for this.) Copy the entire state script into a text editing program. On '''Macs''', you'll have to '''drag the blocked text and drop it''' into the text editor program. Save the state script into a file named e.g. yourMolecule_state.spt in the yourMolecule folder. The file type '''.spt''' signifies that this is a Jmol script. Be sure to save it as plain text. On Macs, plain text editors are TextEdit (comes with OS X; select ''Make Plain Text'' on the ''Format'' menu), and TextWrangler (free from [http://barebonessoftware.com BareBoneSoftware]). On Windows, you could use WordPad (select ''Text Document'' on the ''save as type'' menu), Notepad, or MS Word (select ''Plain Text'' on the ''save as type'' menu). | ||
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'''Disable the ''load'' command:''' Put a hash sign (#) before the load command in the state script. You will find this command at the end of the second block of commands, namely, at the end of the block that begins "function _setFileState() {". Prefixing "#" comments it out", disabling it. The result should look something like this: | |||
: #load /*file*/"http://proteopedia.org/cgi-bin/getpdbz?3ckz"; | |||
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'''Put Jmol.jar in ''yourMolecule'' folder.''' Download Jmol: At [http://jmol.org Jmol.Org], select Download (upper right), go to the Jmol Downloads Page, and download the current version as a binary.zip file. Unzip the file (this is automatic on Macs), and copy the file Jmol.jar. This is the Jmol application. Paste Jmol.jar into yourMolecule folder. | |||
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Put a copy of the [[PDB file]] used in your module in the ''yourMolecule'' folder. In Proteopedia, search for your [[PDB code]], and on the page titled with that PDB code, use the ''coordinates: save as pdb'' link to download the file. | Put a copy of the [[PDB file]] used in your module in the ''yourMolecule'' folder. In Proteopedia, search for your [[PDB code]], and on the page titled with that PDB code, use the ''coordinates: save as pdb'' link to download the file. | ||
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'''Open Jmol:''' You should now have 3 files in yourMolecule folder: Jmol.jar, a PDB file which we'll refer to as yourMolecule.pdb, and a yourMolecule_state.spt file. Double-click Jmol.jar, and a black window will appear titled "Jmol". If the white "Jmol Script Console" window does not appear, use Jmol's File menu, Output Console to open it. | |||
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'''Display your scene:''' Type "load yourMolecule.pdb" | |||
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