Help:Uploading molecules: Difference between revisions
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This article gives step by step instructions for uploading an [[atomic coordinate file]] (a "molecule" or [[PDB file]]) for use in molecular scenes in Proteopedia. | This article gives step by step instructions for uploading an [[atomic coordinate file]] (a "molecule" or [[PDB file]]) for use in molecular scenes in Proteopedia. For uploading other types of files, see [[Help:Multimedia]]. | ||
This article assumes you are familiar with Proteopedia's [[Scene authoring tools|Molecular Scene Authoring Tools]] ([[SAT]]). If you want to improve your familiarity with the SAT, the best place to start is with the [[Proteopedia:Video_Guide|Video Guides]]. | This article assumes you are familiar with Proteopedia's [[Scene authoring tools|Molecular Scene Authoring Tools]] ([[SAT]]). If you want to improve your familiarity with the SAT, the best place to start is with the [[Proteopedia:Video_Guide|Video Guides]]. | ||
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'''Show the Scene Authoring Tools'''. | '''Show the Scene Authoring Tools'''. | ||
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In the '''load molecule''' dialog, '''paste''' the full filename of your uploaded molecule into the slot labeled ''From Proteopedia uploaded file''. Click the ''load'' button. Momentarily, you should see your uploaded molecule in the SAT's Jmol. Color and render as desired, and save the scene to a green link as shown in the [[Proteopedia:Video Guide|Video Guides]]. | In the '''load molecule''' dialog, '''paste''' the full filename of your uploaded molecule into the slot labeled ''From Proteopedia uploaded file''. The name should not include the final '.gz' extension; be careful too with underscores in the filename, which may have been converted to spaces; make sure to use the underscore. Click the ''load'' button. Momentarily, you should see your uploaded molecule in the SAT's Jmol. Color and render as desired, and save the scene to a green link as shown in the [[Proteopedia:Video Guide|Video Guides]]. | ||
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'''Theoretical models''': If your model is a macromolecule [[Theoretical models|generated from theory (ab initio, homology modeling)]], copy the template below and paste it into the very top of your page. | '''Theoretical models''': If your model is a macromolecule [[Theoretical models|generated from theory (ab initio, homology modeling)]], copy the template below and paste it into the very top of your page. | ||
<nowiki>{{Theoretical_model}}</nowiki> | |||
This will display a cautionary banner at the top of your page, like the one at the top of [[Structure of E. coli DnaC helicase loader]]. If your model was determined by empirical experiment, such as [[X-ray crystallography]] or [[NMR]], or if it is a small molecule (less than 100 atoms), it is not necessary to include this caution. | This will display a cautionary banner at the top of your page, like the one at the top of [[Structure of E. coli DnaC helicase loader]]. If your model was determined by empirical experiment, such as [[X-ray crystallography]] or [[NMR]], or if it is a small molecule (less than 100 atoms), it is not necessary to include this caution. | ||
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** An option for Windows-users is downloading [http://www.umass.edu/microbio/rasmol/pdbtools.htm Eric Martz's PDB Tools] and using an included MS-DOS program, alphac.exe. This program keeps alpha carbons and phosphorus atoms from nucleic acids. | ** An option for Windows-users is downloading [http://www.umass.edu/microbio/rasmol/pdbtools.htm Eric Martz's PDB Tools] and using an included MS-DOS program, alphac.exe. This program keeps alpha carbons and phosphorus atoms from nucleic acids. | ||
** Michael Palmer's [http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ MakeMultimer] has an option to return only backbone atoms (4 atoms per amino acid instead of a single alpha carbon atom). It also returns nucleic acid backbones (6 atoms per nucleotide). | ** Michael Palmer's [http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ MakeMultimer] has an option to return only backbone atoms (4 atoms per amino acid instead of a single alpha carbon atom). It also returns nucleic acid backbones (6 atoms per nucleotide). | ||
* For important residues, the full information can be added back to the reduced PDB file, by re-inserting portions of the original source PDB file. | * For important residues, the full information can be added back to the reduced PDB file, by re-inserting portions of the original source PDB file using a [[Help:Plain text editors|text editor]]. | ||
* Appropriate names for such a file may include the letters ''ca'' and the alterations should be clearly noted in the description. You should also note the modifications on the actual Proteopedia page where the file is displayed, as the modifications may substantially affect possible views that other users may generate using your file. | * Appropriate names for such a file may include the letters ''ca'' and the alterations should be clearly noted in the description. You should also note the modifications on the actual Proteopedia page where the file is displayed, as the modifications may substantially affect possible views that other users may generate using your file. | ||
See '[[Jmol/Visualizing large molecules|Visualizing large molecules]]' for additional tips and solutions for dealing with issues related to PDB file size. | See '[[Jmol/Visualizing large molecules|Visualizing large molecules]]' for additional tips and solutions for dealing with issues related to PDB file size. | ||
