Help:Uploading molecules: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Angel Herraez, Jaime Prilusky, Karsten Theis

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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]].
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 If the molecule you want to display is available from the [[Protein Data Bank]], you don't need to upload it. In the ''load molecule'' dialog of the [[Scene authoring tools|Molecular Scene Authoring Tools]] ([[SAT]]), simply give the [[PDB code]], and Proteopedia will obtain the PDB file for you.
+:In fact, Proteopedia will automatically make a frozen copy of the current PDB entry for you. This will prevent your green links from being broken by future remediations of data files in the [[Protein Data Bank]].
 =Don't upload a file unless you have permission!=
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 '''Compress''' the PDB file, especially if it is more than ~200 kilobytes in size. Use WinZip in Windows, Finder's "compress" in Mac OS X, or gzip. Files compressed by these methods are recognized and decompressed automatically by Jmol. If you're not sure about your compression method, simply try dragging the compressed PDB file and dropping it into the black window of the [[Jmol/Application|Jmol application]]. If the molecule appears, Jmol decompressed it automatically.
 </li><li>
-Click '''Upload file''' in the ''toolbox'' at the bottom of the left side of every page in Proteopedia. Choose the file to be uploaded from your disk. Do NOTclick the upload button yet.
+Click '''Upload file''' in the ''toolbox'' at the bottom of the left side of every page in Proteopedia. Choose the file to be uploaded from your disk. Do NOT click the upload button yet.
 </li><li>
 Choose a '''file name''' carefully and put it in the ''Destination filename'' slot. The filename should be unique enough to distinguish it from all the other hundreds of files uploaded into Proteopedia, and descriptive enough to identify it. Do not include spaces in the filename -- use underscores or dashes to separate words. The filename should end in '''.pdb''' (or another file type that identifies the data format), or if compressed, '''.pdb.zip''' or the filetype that identifies the compression method.
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 :If (and only if!) you are uploading an unpublished PDB file that is to be hidden until the date of publication, the filename should begin with "Workbench_" (see [[Proteopedia:Workbench]]).
-Good filenames (unique, descriptive):
+Good filename examples (unique, descriptive):
-<ul><li>
+<ul><ul><li>
-[[Image:Taxa_4_11_dien_5A_13A_diol.pdb]]
+[[:Image:1abb_693-696.pdb|1abb_693-696.pdb]]
-</li></ul>
+</li><li>
+[[:Image:Taxa_4_11_dien_5A_13A_diol.pdb|Taxa_4_11_dien_5A_13A_diol.pdb]]
+</li><li>
+[[:Image:1qx3.3kjf.morph.pdb]]
+</li><li>
+[[:Image:2hf3_crystal_packing_39_50_around12_selected.pdb|2hf3_crystal_packing_39_50_around12_selected.pdb]]
+</li></ul></ul>
-Poor filenames (too general, not descriptive):
+Poor filename examples (too general, not descriptive):
 <ul><ul><li>
-[[Image:X.pdb]]
+[[:Image:X.pdb|X.pdb]]
 </li><li>
-[[Image:Chain_b.pdb]]
+[[:Image:File1.pdb|File1.pdb]]
 </li><li>
-[[Image:Complex.pdb]]
+[[:Image:Chain_b.pdb|Chain_b.pdb]]
 </li><li>
-[[Image:1A6Z.pdb.gz]] (NO uploaded file should have the same name as a published [[PDB]] entry.)
+[[:Image:Complex.pdb|Complex.pdb]]
+</li><li>
+[[:Image:1A6Z.pdb.gz|1A6Z.pdb.gz]] (NO uploaded file should have the same name as a published [[PDB]] entry. Simply give the 4-character [[PDB code]] in the [[SAT]] and the PDB file will be retrieved automatically.)
 </li></ul></ul>
@@ Line 57: / Line 67: @@
 </li></ol>
-=Create a molecular scene showing the uploaded PDB file=
+=How to create a molecular scene showing the uploaded PDB file=
-<ol><li>
+<ol start="7"><li>
 '''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. Click on your name at the top of the window. This takes you to your User page.
+: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''.
 </li><li>
+'''Edit''' the page where you want to show the molecule.
+:If you are unclear about editing pages, inserting Jmol with the 3D button, and using the [[SAT]], please review the [[Proteopedia:Video Guide|relevant video guides]].
 </li><li>
+'''Show the Scene Authoring Tools'''.
 </li><li>
+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]].
 </li><li>
+'''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.
 </li></ol>
+=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 extract only the alpha carbons include:
+**Use the 'Pick C&alpha;, 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.