File talk:Protein CREBBP PDB 1f81.png

Disputed

As the PDB page http://www.pdb.org/pdb/explore/explore.do?pdbId=1f81 says, this is amino acids 1764-1850 from the mouse's CBP, so it shows only 86 of all 2400 amino acids. You should either make that clear or replace the picture. Hint: there is still no structure showing the full human protein! --Ayacop (talk) 19:30, 6 March 2012 (UTC)

Thanks for bringing this to my attention. I agree that the statement "Structure of the CREBBP protein." in this file's description isn't as precise as it could be. The statement is imprecise in that it could be plausibly interpreted to mean the structure is of the entire protein, even though the corresponding PDB file is for a fragment of the CREBBP protein. This is a potential issue in ~2,500 other protein structure images uploaded by PDBbot. Ideally, the form of the revised wording would be automatically generatable from structured data in resources like PDB entries. If you have any suggestions for the revised wording, please let me know. Best, Emw (talk) 17:36, 10 March 2012 (UTC)

Just state which amino acids are shown and which organism. That PDBbot images are generally unusable does not make the problem go away. At least in WP-de, we refrain from presenting such incomplete pictures at the article top, implying "This is IT". Maybe you need such a policy in WP-en too? --Ayacop (talk) 08:31, 11 March 2012 (UTC)

Stating the expressing organism would be a good idea, but only stating the amino acids shown seems too low-level. I have expanded the image's description here. Please let me know if you think it could be improved, and if so how.

I disagree with the notion that the PDBbot images are "generally unusable" for a few reasons: 1) the captions on the images in the corresponding articles are accurate and precise (e.g. "PDB rendering based on 1f81"; see here), and 2) the issue with statements of the form "Structure of the CREBBP protein" -- which are likely read by only a very small fraction of those who view the image -- is one of a degree of precision. PDB 1f81 is a fragment, but it is of the CREB-binding protein, contradicting the statement "PDB 1F81 is not Creb (sic) binding protein" in your dispute. So I think the issue might not be quite as egregious as you seem to suggest. In any case, I will run a proposal for improved wording in PDBbot image descriptions by the people at Gene Wiki, and will implement a fix for those descriptions soon. Thanks again, Emw (talk) 15:54, 11 March 2012 (UTC)

The new description is fine with me, except that instead of "expression organism" the mouse is the actual organism where that specific protein is from. The expression organism, i.e., where the protein was amplified to get a crystal, is with this PDB, in fact, E. coli. I don't think you should state the expression organism but you should give the organism of the protein! Again, this is not the human CREBBP but mouse CREBBP.

As to whether I'm splitting hairs, you are free to present what you want as "the CREBBP". If that's actually educational then, is another matter. You won't help people's understanding by hiding important facts, and presenting a small(!) part of a thing and not saying so will confuse the most willing student. --Ayacop (talk) 09:14, 14 March 2012 (UTC)

It hadn't occurred to me that PDB image captions of the form 'PDB rendering of 1f81' as seen on actual gene/protein articles might also be confusing because of their brevity. I think there's merit to that critique. And I appreciate the copyediting about my ambiguous use of expression. I've forwarded both of these inputs to the discussion about improving the PDB images at Gene Wiki here. Emw (talk) 17:52, 25 March 2012 (UTC)