Comments on Protein Data Base, The Internet is for everyone, not just who you are familiar with

I was just browsing Protein Data Base PDB and wanted to look at the electron density at https://www.rcsb.org/structure/1bkv

It timed out, so I looked at Chrome Devtools consoles to see

loadSearch: counter.n=37
react-search.js?ts=5455752:138 loadSearch: counter.n=38
react-search.js?ts=5455752:138 loadSearch: counter.n=39
react-search.js?ts=5455752:153 ERROR: UNABLE TO LOAD SEARCH COMPONENT AFTER 40 ATTEMPTS

May be unrelated to display (lack of) 3D structures, but just wanted you to know, clicking on buttons below the 2D structure times out.

The links that are not responding:

https://www.rcsb.org/3d-view/1BKV?preset=electronDensityMaps
https://www.rcsb.org/3d-view/1BKV/1

This loaded eventually but no structure.
https://www.rcsb.org/3d-view/1BKV?preset=ligandInteraction&label_asym_id=D

Switched to JsMol and something comes up. There are about 4.8 Billion people with some access to the Internet, and they are likely to dig into these things eventually. There will be many more first time visitors, especially if they abandon the browse because nothing works. Or appears to.

After waiting long enough, and switching to JSmol after the delay, I could get something.

Recommend. Test JSMOL and other viewers for first time visitors and occasional visitors. Let them choose a default view. Do not make them log in, but offer them “community” if they do register. There will be more viewers and people wanting compare, then one who want to play with programming. [ You are too heavy on “graduate student” bias. Most people do not have time to spend weeks playing with clumsy interfaces because you do not value their time.] I put that in [] because it is partly a joke about the uses and abuses of graduate students, but a truth about most of the Internet.

Thanks for the hard work. But from my perspective (all 7.8 Billion people, and 4.8 Billion who might be able to get here) you have a long way to go to be universally user friendly. And that does not mean you have to dumb down the content, just simplify the interface so that it is language and age and background independent. Start with what people can see and interact with. Most of these proteins are shown in isolation – unconnected to the communities and uses and impacts and applications in society.

I would like to see the cartoon, secondary structure, solvent AND solvent excluded (1) side by side (2) overlaid transparently.

You are wasting a lot of screen space on things that can be minimized or not shown at all.  You expect only people who have taken years or decades to memorize the context will use your site. But its greatest use is for people and groups where you provide a clear framework — without introducing limitations. Personally, I don’t think you can do it. But I hope I am wrong.

Right Click drag is often used for move or pan. If you would let people put multiple structure on the same screen, save them, overlay and compare them, save views, share views, those are things many communities can use.

“protein” is 834 Million entry points (Google, GMT 12 Nov 2021, 2:27 pm)
(“protein structure” OR “protein structures”) has 15.3 Million entry points

And you provide no map or guide or view of that at all.

You expect only people who have taken years or decades to memorize the context will use your site. But its greatest use is for people and groups where you provide a clear framework — without introducing limitations. Personally, I don’t think you can do it. But I hope I am wrong.

site:rcsb.org has 649,000 entry pages.

Do you really think you are doing the Internet users a favor by leaving your site as that many “paper pages” in English with links and no conceptual framework or tools for managing that view of the world? When sites accumulate that many entry points, the usefulness drops, user time wasted grows, and total lost time on the internet for the most difficult problems becomes factorial.

I am not beating up on you. Just mentioning some serious things I have found in the last 24 years of the Internet Foundation, trying to trace out why all global issues are not closing out and those people moving on to more serious problems.

Your institution type, role and research interest categories show the very narrow view you are using for who might visit. If you put it on the Internet, it is for everyone, not just who you are familiar with.

Richard Collins, Director, The Internet Foundation

Richard K Collins

About: Richard K Collins

Director, The Internet Foundation Studying formation and optimized collaboration of global communities. Applying the Internet to solve global problems and build sustainable communities. Internet policies, standards and best practices.


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