Curved helix tubes

[olibclarke@…]

Begin forwarded message:

From: Oliver Clarke
Subject: Possible enhancements to ribbon style editor for ChimeraX
Date: February 15, 2016 at 1:36:39 PM PST
To: Tom Goddard

...

• Also, if there is any way to create a "curved cylinder" representation for helices, applied as a ribbon style rather than as per pipes and planks, I really think it is essential - having good reduced representations of molecules that preserve as much information as possible is increasingly important as solved structures become larger and more complex. E.g. check out the number of curved helices in the attached structure - ribbons are not optimal because it is so big, but pipes and planks looks like a mess...

Cheers,
Oli.

[Elaine Meng]

Begin forwarded message:

From: Oliver Clarke <>
Subject: Re: ChimeraX suggestion - forward/back depth cueing ramps
Date: May 26, 2016 at 11:50:48 AM PDT
To: Tom Goddard

Also, I still think curved helices (e.g. as in Cuemol - ​http://www.cuemol.org/en/index.php?Gallery - but perhaps they could be implemented better) would be a great addition to ChimeraX as a different representation style - helical ribbons themselves add visual clutter to structures of large molecules, and pipes-and-planks is a bit too crude for such figures. Possibly the attached paper might be useful at some point for implementing curved helices in a way that is more simplified than a simple sliding window approach, but with a little more fidelity to the underlying structure than a series of rigid cylinders? Anyway, as usual take or leave, just a thought.

Cheers,
Oli.

[Conrad Huang]

Try "cartoon style modehelix tube". There are plans for similar options for strands but those have not been implemented yet.

[olibclarke@…]

That’s what I am doing, and I really like the representation - the issue is that the interface frequently becomes unresponsive for several minutes when using "modehelix tube”, but not with the regular cartoon representation (at least with my structures, which admittedly are on the large side).

Oli

[olibclarke@…]

Thanks! This works great now. Also, whatever issue was making ChimeraX unusable (due to frequent freeze-ups) on my MBP without discrete graphics seems to be fixed in this build. There are still glitches in representation of some helices (making them much too fat) which you can see in the attached PDB if you run dssp first, but overall I really like the representation!

Cheers
Oliver.

cam_jan20.pdb​

[olibclarke@…]

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[Conrad Huang]

Many other ribbon tickets still open.