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ncbi / icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode
https://www.ncbi.nlm.nih.gov/Structure/icn3d
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Spectrum coloring #39

Closed digitalbio closed 3 years ago

digitalbio commented 3 years ago

Cn3D has a Rainbow coloring style that colors chains from the 5' end to the 3' end, or the amino end to the carboxyl end with the order ROYGBIV. ( red orange yellow blue indigo violet)

I noticed today that this order is reversed when I use the Spectrum color in iCn3D. Is there a reason why the order has changed? If there isn't a good reason, can this be changed back to ROYGBIV like it was in Cn3D?

youkha commented 3 years ago

this is the correct rainbow if you look at rainbows ... I think pymol uses the reverse but not other shrodinger software ... we could think of having both but you may want to check across multiple software first

On Wed, Jul 28, 2021 at 2:26 AM Sandra Porter @.***> wrote:

Cn3D has a Rainbow coloring style that colors chains from the 5' end to the 3' end, or the amino end to the carboxyl end with the order ROYGBIV. ( red orange yellow blue indigo violet)

I noticed today that this order is reversed when I use the Spectrum color in iCn3D. Is there a reason why the order has changed? If there isn't a good reason, can this be changed back to ROYGBIV like it was in Cn3D?

— 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/39, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD35NIKD3FQZYJT2QXATXQLTZ5FCHANCNFSM5BDI475A .

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digitalbio commented 3 years ago

I have found that my students can understand the order ROYGBIV. I’m worried that having this in reverse order will confuse them.

Maybe, a way around this would be to have a Rainbow coloring mode in addition to the Spectrum mode. That way we could use the Rainbow mode in an education version and the pymol users could stick with with Spectrum.

Sandy

On Jul 28, 2021, at 4:38 AM, Philippe Youkharibache @.***> wrote:

 this is the correct rainbow if you look at rainbows ... I think pymol uses the reverse but not other shrodinger software ... we could think of having both but you may want to check across multiple software first

On Wed, Jul 28, 2021 at 2:26 AM Sandra Porter @.***> wrote:

Cn3D has a Rainbow coloring style that colors chains from the 5' end to the 3' end, or the amino end to the carboxyl end with the order ROYGBIV. ( red orange yellow blue indigo violet)

I noticed today that this order is reversed when I use the Spectrum color in iCn3D. Is there a reason why the order has changed? If there isn't a good reason, can this be changed back to ROYGBIV like it was in Cn3D?

— 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/39, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD35NIKD3FQZYJT2QXATXQLTZ5FCHANCNFSM5BDI475A .

-- -- Philippe Youkharibache, Ph.D. US +1 415 448 6509 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

jiywang3 commented 3 years ago

@digitalbio A good question. Most 3D viewers (I checked PYMOL, JMOL, Miew, etc) use a reversed order of the rainbow. Maybe the reason is to be consistent with the DNA order, which is the reverse order of mRNA? I just used the convention. Let me think about it.

digitalbio commented 3 years ago

No, that’s not quite right.

The mRNA is in the same order as the coding sequence of the DNA.

The template strand of the DNA is in the reverse order.

When we teach about the relationship between DNA sequences, mRNA, and proteins, we always talk about these in terms of 5’ to 3’ using the + sense of the RNA. I think that’s probably why Cn3D uses rainbow coloring.

So:

DNA 5' ---> 3' mRNA 5' ----> 3' protein NH3+ -----> COO-

We want students to know that direction is very important in biology - DNA replication, transcription, and translation all go in a 5' to 3' direction.

Anyway - I think the way to resolve this issue is to add a Rainbow coloring mode. That way, teachers can use the Rainbow mode (ROYGBIV 5' > 3' amino > carboxyl ) in a way that's easier for students to understand and the protein chemists can use Spectrum with the other orientation. The two names help prevent confusion.

On Jul 29, 2021, at 10:18 AM, Jiyao Wang @.***> wrote:

@digitalbio A good question. Most 3D viewers (I checked PYMOL, JMOL, Miew, etc) use a reversed order of the rainbow. Maybe the reason is to be consistent with the DNA order, which is the reverse order of mRNA? I just used the convention. Let me think about it.

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jiywang3 commented 3 years ago

The color method "Rainbow" was just released. Thanks!