Molecular Playground/Procedures: Difference between revisions
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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 (one of a large number of files in the zipped download). This is the Jmol application. Paste Jmol.jar into yourMolecule folder. | '''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 (one of a large number of files in the zipped download). This is the Jmol application. Paste Jmol.jar into yourMolecule folder. | ||
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'''Add the PDB file:''' Put a copy of the [[PDB file]] featured 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. | '''Add the PDB file:''' Put a copy of the [[PDB file]] featured 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. Rename the file to ''yourMolecule.pdb''. It will help if all the filenames in your module contain the name of your molecule. | ||
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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. | '''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. | ||
