[chimerax-users] smoothen coils

[Gabor PAPAI]

Thank you Elaine, this works well. Luckily I don’t have strands in the structure I want to depict like this.

Best regards,
Gabor
---
Gabor Papai
IGBMC
Integrated Structural Biology
1, rue Laurent Fries, Bp 10142
67404 Illkirch, France
Tel: +33-3-69485288

On 10 May 2019, at 18:38 , Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

One really bad hack for now is to reassign all the coil as strand so that it gets smoothed and then show all strand as licorice (thin tube), but that is not a solution if the structure has “real” strands that you want to show with arrows.

open 2gbp
cartoon style helix modeh tube radius 1.5
setattr coil residue is_strand true
cartoon style ~helix xsection round width 1 thick 1 arrows f
open 2gbp

(second copy is to compare smoothed and unsmoothed “coil” position)

Elaine

On May 10, 2019, at 9:15 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Gabor,
Currently there is no option of “cartoon” to smooth the coils, so this would have to go on the request list.  There is a “smooth” option, but it applies only to peptide beta-strands:

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>

Sorry about that,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. while it does not address your question, you may be interested that we added a preset with tube helices (Presets… Cylinders/Stubs)

On May 10, 2019, at 8:23 AM, Gabor PAPAI <papai at igbmc.fr<mailto:papai at igbmc.fr>> wrote:

Dear developers,
I would like to show helices as tubes (this I know how to do) and coils between them with smooth trajectories, more schematic, as it is drawn in Chimera using Pipes and Planks (or even more).
I would appreciate your help!
Best regards,
Gabor


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