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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'''Copy''' the full filename as shown in the title of the uploaded file page. | '''Copy''' the full filename as shown in the title of the uploaded file page. | ||
:If you don't have the full uploaded filename in front of you, here is how you can find it. | :If you don't have the full uploaded filename in front of you, here is how you can find it. Be sure to sign in to Proteopedia and then click on your name at the top of the window. This takes you to your User page. In the ''toolbox'' (lower left on every page in Proteopedia) click on ''User contributions''. On that page, change ''namespace'' from ''All'' to ''Image''. Click ''Go''. | ||
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'''Edit''' the page where you want to show the molecule. | '''Edit''' the page where you want to show the molecule. | ||
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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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=Additional considerations for large files= | =Additional considerations for large files= | ||
For very large files, such as large [[Complexes|complexes]] or [[Morphs|morphs]], you may wish to take steps to reduce file size further prior to using file compression. In the end, the scene using your upload PDB file should load for a user in a reasonable amount of time. The best way to do this is to exclude portions of the PDB file not critical to scenes you will generate. Generally, one can save just the alpha carbons of the protein residues as Jmol can still represent the proteins in many forms, including cartoon, backbone, trace, and ribbons. Ways to | For very large files, such as large [[Complexes|complexes]] or [[Morphs|morphs]], you may wish to take steps to reduce file size further prior to using file compression. In the end, the scene using your upload PDB file should load for a user in a reasonable amount of time. The best way to do this is to exclude portions of the PDB file not critical to scenes you will generate. Generally, one can save just the alpha carbons of the protein residues as Jmol can still represent the proteins in many forms, including cartoon, backbone, trace, and ribbons. | ||
Appropriate names for such a file may include the letters ' | * Ways to extract only the alpha carbons include: | ||
**Use the 'Pick Cα, backbone and side chain atoms' option at [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/index.html PDB Goodies]. | |||
**Use a filter in the load command in the [[Jmol/Application|Jmol application]] to load only the alpha carbons, and then write a new file with the coordinates. [[Jmol/Visualizing large molecules#Displaying Only Alpha Carbon Atoms|Here are '''instructions'''.]] | |||
** 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). | |||
* 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. | |||
See '[[Jmol/Visualizing large molecules|Visualizing large molecules]]' for additional tips and solutions for dealing with issues related to PDB file size. | |||