The membrane information should be hidden by default

[digitalbio]

Structure 1LQQ

The red and blue objects should not be visible unless a user wants to see them. These are very confusing for students and an unpleasant surprise for instructors who aren't expecting this problem.

[youkha]

JIYAO. Please NO ... many requests are OK but some are not when presented as "the" option. We may want to improve Preferences. That may be the right way to address some demands. and we may want to request our users also to propose and think about how to improve for all not just for their preferences to be the option of even the default but allow them to set preference and their defaults.

SANDRA. please consider when you have a request that you may not speak for all, certainly here not for me or for many users dealing with membrane proteins. This example might be a little weird as the structure seems above the extracellular (red) membrane ... not sure what it is if a bug or if simply a membrane surface protein domain ... it is extremely important that people know when a structure is a membrane protein and its position vs a membrane, and if some info should be available to students, their teachers and researchers all among 135,000 users.

Jiyao is very cooperative and sometimes overrides even my choices with others' choices . We have been developing iCn3D with that interactive mode but we need a minimum of balancing now that a new generation of active users is developing OK. So please always consider that your choices are subjective and try to see if you can propose something that fits diverse choices. This can be a PREFERENCE not a dictat.

I am glad Sandra and others use the software for students and provide input. In fact, I am glad I am not always the bearer of bad news with bugs or that I am not the only one ... BUT we need a process here to balance requests and evaluate them.

SORRY if I have not been more active lately in channelling and tampering requests and making them more universal, but we need some level of understanding on how to enable users requests for the community as a whole and projecting with future developments.

Philippe

On Wed, Nov 24, 2021 at 5:21 PM Sandra Porter @.***> wrote:

Structure 1LQQ

The red and blue objects should not be visible unless a user wants to see them. These are very confusing for students and an unpleasant surprise for instructors who aren't expecting this problem.

[image: Screen Shot 2021-11-24 at 2 20 07 PM] https://user-images.githubusercontent.com/6663433/143319989-53efd01e-e79d-42cb-b38f-fd458d148ab1.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ncbi/icn3d/issues/72, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD35NIJAORC4EEASHWM26JTUNVQQFANCNFSM5IXD2AAA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- -- Philippe Youkharibache, Ph.D. US +1 415 448 6509

[jiywang3]

Yes, this is a good case to use Preferences. The membrane will be shown by default since it carries important information for biologists. Users could change the Preferences to hide it by default.

[digitalbio]

I disagree. Here's why I think the red and blue discs should be hidden by default:

1. The structure I reported, LQQ, is not a membrane protein.

2. It's easy to find structures like 5VBL that are membrane proteins where the weird discs do not appear on loading. And the Toggle Membrane feature is not available.

3. We did not have to work hard to find these two examples.

4. The NCBI records in the MMDB do not show these discs. I think it makes more sense to click an image at the NCBI and see the same image appear in iCn3D.

5. It is confusing to users to have these discs appear in structures, seemingly at random. I think you should look at the image in GitHub before drawing conclusions.

I am happy discuss this.

[jiywang3]

I implemented "Show Membrane" in the menu "Style > Preferences". By default the membrane will be shown if it's available. Users could modify the Preferences as they like.

[digitalbio]

This should really be the other way around with membrane objects hidden by default.

Our students don't know what these disc-like objects are. We didn't know what they were until Aron told us.

We should not be introducing new objects into structures unless the users want to see them.

I think this is something that should be turned on in Preferences and not on by default.

[youkha]

Too much talk here sorry the solution is preferences meaning users set THEIR defaults tgat is what prefernces are. What is there else to discuss.

We would slso need volunteers to help ckeanup data wher it is needed

On Wed, Nov 24, 2021 at 7:55 PM Sandra Porter @.***> wrote:

This should really be the other way around with membrane objects hidden by default.

Our students don't know what these disc-like objects are. We didn't know this.

We shouldn't be introducing new objects into structures unless the users want to see them. I think this is something that should be turned on in Preferences and not on by default.

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/ncbi/icn3d/issues/72#issuecomment-978659745, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD35NIM4QWUCVCLWZGMTJPLUNWCR5ANCNFSM5IXD2AAA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- -- Philippe Youkharibache, Ph.D. US +1 415 448 6509

[jiywang3]

I fixed the membrane data of 5VBL. Now it's showing up: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=5VBL