Help:Uploading molecules

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 assumes you are familiar with Proteopedia's Molecular Scene Authoring Tools (SAT). If you want to improve your familiarity with the SAT, the best place to start is with the Video Guides.

Don't upload files available from www.pdb.orgDon't upload files available from www.pdb.org

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 Molecular Scene Authoring Tools (SAT), simply give the PDB code, and Proteopedia will obtain the PDB file for you.

Don't upload a file unless you have permission!Don't upload a file unless you have permission!

Once a file is uploaded to Proteopedia, it becomes publicly available and anyone can view it and download it.

• If the file is one you created entirely from your own work, it is OK to upload it.
• If the file is the work of others, or derived from the work of others, be sure that you have permission to share it publicly before uploading it to Proteopedia. And of course you must properly cite the original work.
• If the file is based upon, or derived from, files published in the Protein Data Bank (www.pdb.org) you do not need explicit permission from the authors, but of course you must properly cite the original work. This can be done either by providing links to the original PDB codes in your Proteopedia article, or by directly citing the relevant publications.
  • The wikitext for linking to PDB code 1d66 is [[1d66]]. The link looks like this: 1d66.
  • Here are instructions for citing scientific literature.

Please see also Proteopedia:Guidelines for Ethical Writing.

Uploading a file from www.pdb.org after modifying itUploading a file from www.pdb.org after modifying it

If you want to upload a modified version of a file available from the Protein Data Bank, please indicate the modification in the filename. For example, there are eight chains in the asymmetric unit of 3zsf, but it is believed that the functional form, the biological assembly, is a single chain. So you might want to delete chains B, C, D, E, F, G, and H from 3zsf.pdb (downloaded from the PDB), and upload a file containing only chain A. Please do not name your modified version 3zsf.pdb because that name conflicts with the published, eight-chain version of the file. Give your uploaded file a name that indicates the modification, such as 3zsf_chain_a.pdb.

How to upload a PDB fileHow to upload a PDB file

These instructions refer to PDB files, but the format of the atomic coordinate file does not matter. It can be cif, xyz, or any of the 40-some atomic coordinate file formats readable by Jmol.

1. Watch the short video that demonstrates uploading a file. The video concerns an image file, but will still be quite helpful. The steps below concern a PDB file or "molecule".
2. 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. If the molecule appears, Jmol decompressed it automatically.
3. 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.
4. 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.

   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 filename examples (unique, descriptive):
   • 1abb_693-696.pdb
   • Taxa_4_11_dien_5A_13A_diol.pdb
   • Image:1qx3.3kjf.morph.pdb
   • 2hf3_crystal_packing_39_50_around12_selected.pdb

   Poor filename examples (too general, not descriptive):

   • X.pdb
   • File1.pdb
   • Chain_b.pdb
   • Complex.pdb
   • 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.)
5. Describe the contents of the file in the Summary box. You could tell how it was obtained or generated, cite the source, and specify any restrictions on the use of the file imposed by the copyright holder. If the filename includes a PDB code, explain how the contents differ from the published PDB entry.
6. Click the Upload file button. You will next see a page about the uploaded file. In Proteopedia, every uploaded file (regardless of the type of content) is stored in the Image: namespace.

Create a molecular scene showing the uploaded PDB fileCreate a molecular scene showing the uploaded PDB file

1. 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.