Proteopedia:Policy

Links to WikipediaLinks to Wikipedia

1. Most topics should have their own page in Proteopedia, even if initially that page contains nothing but a link to the corresponding page on the topic in Wikipedia
2. If the page exists within Proteopedia, you should link to it, and not to Wikipedia.
3. If the page topic is a protein or a molecule, especially one that could benefit from Jmol applets and scenes to describe it structurally, then a "red" link to an empty page in Proteopedia might encourage someone to create the page within Proteopedia, and should be created.
4. The name of a crystallographer should link within Proteopedia and that page may contain a link to her/his entry in Wikipedia if it exists.
5. When Wikipedia has an article relevant to Proteopedia, one should never hesitate to link to Wikipedia. However, such links to Wikipedia should nearly always be made on a page with the same topic in Proteopedia. There is no reason to duplicate what is in Wikipedia within Proteopedia. However, often Proteopedia may wish to emphasize or summarize specific aspects of a topic, whereas Wikipedia will attempt to be broad and comprehensive. That is the reason for the following rule.
6. For most topics, and certainly when in doubt, it is better to create a new page within Proteopedia, and then put a link to Wikipedia on that Proteopedia page on the same topic. This provides a place to emphasize aspects of the topic important to Proteopedia, even though these aspects may be mentioned somewhere in Wikipedia's article. For example, the Proteopedia page on the Protein Data Bank could emphasize that new entries are released weekly, and that following each weekly release, new Proteopedia pages are created for each new entry automatically, a process called "seeding". However, the Proteopedia page on the Protein Data Bank need not repeat everything that Wikipedia says, and should certainly link to the Wikipedia article for more information. Also, we don't want to scatter links to Wikipedia's articles throughout Proteopedia articles, and then later realize it would have been better to have all those links go to to a Proteopedia article (which in turn links to Wikipedia). This would probably create a maintenance problem, trying to find and update all those links.
7. If the page is unrelated to proteins or molecules (like a page for an organism), and the page exists and is useful within Wikipedia, you may link directly to Wikipedia.

Avoid Obscure Page TitlesAvoid Obscure Page Titles

Please avoid using titles for new Topic pages that will not be meaningful to non-specialists. For example, titles that are specialist acronyms such as SGAP, Cyt2Ba, Nqo1, and VirE1/VirE2 will not be meaningful to most users of Proteopedia. Using the move tab, these pages have been retitled. When a page is moved (renamed), a redirect page is automatically created from the old title -- therefore searching for the old title will still find the page with the new title. That is why clicking a link such as SGAP goes to the longer and more generally meaningful title. You will see that there is a note, just below the title, that you have been redirected.

Please Don't Delete AbstractsPlease Don't Delete Abstracts

Pages titled with a PDB identification code are initially created automatically, and include the Publication Abstract from PubMed copied from the paper reporting the PDB entry. Even if you write a better overview of the paper or the structure, please do not remove the published abstract. It is OK to put manually-created content first, leaving the published abstract at the bottom of the page.

Protected PagesProtected Pages

Any registered user (after logging in) can create protected pages. How? Please see Help:Protected_Pages. Protecting a page means that its author does not have to worry about the content being changed by someone else. However, all content in Proteopedia is freely available to be copied, edited, used and adapted (click on the GNU Free Document License icon at the lower left of the page for details). Therefore, anyone may copy the content of a protected page into a publicly editable page, where it can evolve in true wiki fashion. Equally, you may copy it into your own protected page, where you may edit it to fit your needs. Examples:

• User:Eric_Martz/Nucleosomes is a protected page. Only its author is able to edit it.
• Nucleosomes contains a copy of the content in the above page, plus other material. Any logged-in user can edit this page.

PDB Code in Plain SightPDB Code in Plain Sight

Please make sure that every page shows, in plain sight, the PDB code(s) for the atomic coordinates used in the molecular scenes shown on that page. The standard place to put the PDB code is beneath the molecular scene in the caption to Jmol. If one Jmol is used to show more than one PDB entry, only then should the PDB codes be moved to the text (near the first green links that show them). If you modify the PDB file, it is still important to state the code -- please see the next section.

Altered PDB FilesAltered PDB Files

Any PDB file that has been modified and uploaded to Proteopedia must be noted as such and the modifications explained, preferably in the summary section when uploading the file, as well as in the page where the modified PDB file appears. If you prefer to make the note explaining the modifications less obtrusive, it can be in a reference footnote.

Theoretical ModelsTheoretical Models

In the broad sense intended here, "theoretical model" means any molecular model that is not derived directly from empirical atomic resolution data, such as crystallographic X-ray diffraction, or a sufficient number of NMR restraints. "Theoretical model" thus includes comparative or homology models, ab initio / de novo models, or any modification to an empirical model, including changes as small as the mutation of a single amino acid.

The positions of sidechains in theoretical models, such as comparative models, or models with theoretically added mutations or changes in conformation, are generally unreliable. The backbone conformation or fold is generally unreliable in ab initio / de novo theoretical models.

No pages in Proteopedia have been automatically generated for the 1,390 theoretical models that were historically deposited in the Protein Data Bank but removed from the main database in 2002. (An example is 1DNN.)

Proteopedia users are free to display an uploaded theoretical model, provided it is clearly identified by including the Theoretical_model banner (by inserting {{Theoretical_model}} at the top of the page), in the caption of the scene, or in the caption of the page (preferably in red) as a Theoretical Model. The wikitext is: '''<font color='red'>Theoretical Model</font>'''

To add the red caption to a scene, use the "labels" tab in the scene authoring tools and open the "caption" section.

An example is a theoretical model that can be displayed on the page for the empirical model 1vzj.