Hi Martin, That is odd, I didn’t know the helix cylinder diameters varied in ChimeraX. I don’t know the algorithm or how to change the diameter. Maybe Conrad (who wrote the code) or Elaine will know. There is a chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list that you can ask such questions on. Tom
On Apr 3, 2017, at 10:40 AM, Martin Moncrieffe wrote:
Hi Tom,
When displaying helices as tubes, can one set the radius of the tubes? I’ve noticed that depending on the structure, the tube diameter is scaled scaled differently even though the docs state that w/h/x-secton do not apply in tube mode. I’m sure you guys have some fancy algorithm to do so.
Anyway, I really like what you’re all doing so far.
Best.
__martin
Hi Martin, Only Conrad knows the details, but it is somehow automatically based on the distance of the CA atoms to the computed midline of the tube. Currently there is no command option to control it. I have also been bothered by this issue and a couple of weeks ago I opened a Chimera ticket (#585) to request that there be an option to set constant radius for these helix tubes. I’ll add your name to the notification list for if/when there is any action on the ticket. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 3, 2017, at 11:07 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Martin,
That is odd, I didn’t know the helix cylinder diameters varied in ChimeraX. I don’t know the algorithm or how to change the diameter. Maybe Conrad (who wrote the code) or Elaine will know. There is a chimerax-users@cgl.ucsf.edu mailing list that you can ask such questions on.
Tom
On Apr 3, 2017, at 10:40 AM, Martin Moncrieffe wrote:
Hi Tom,
When displaying helices as tubes, can one set the radius of the tubes? I’ve noticed that depending on the structure, the tube diameter is scaled scaled differently even though the docs state that w/h/x-secton do not apply in tube mode. I’m sure you guys have some fancy algorithm to do so.
Anyway, I really like what you’re all doing so far.
Best.
__martin
The tube radius is computed from the distances of CA atoms from the center line of the tube. So helices that fit well on the surface of a tube will have the "expected" radius while those that do not fit well typically look fatter (because some CA atoms stray far from the fitted tube surface). We will be adding an option to use a fixed radius rather than the variable one in the next few weeks. Conrad On 4/3/2017 11:07 AM, Tom Goddard wrote:
Hi Martin,
That is odd, I didn’t know the helix cylinder diameters varied in ChimeraX. I don’t know the algorithm or how to change the diameter. Maybe Conrad (who wrote the code) or Elaine will know. There is a chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list that you can ask such questions on.
Tom
On Apr 3, 2017, at 10:40 AM, Martin Moncrieffe wrote:
Hi Tom,
When displaying helices as tubes, can one set the radius of the tubes? I’ve noticed that depending on the structure, the tube diameter is scaled scaled differently even though the docs state that w/h/x-secton do not apply in tube mode. I’m sure you guys have some fancy algorithm to do so.
Anyway, I really like what you’re all doing so far.
Best.
__martin
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participants (3)
-
Conrad Huang -
Elaine Meng -
Tom Goddard