Hi Elaine,
Thanks a lot . Im' still using mostly Chimera (in fact my email was addressed to you I think). Will try. Thanks again
Cedric
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, 19 January 2024 18:02 To: GOVAERTS Cédric Cedric.Govaerts@ulb.be Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: how to measure helix-helix axis angle
Hi Cedric! Happy new year to you too, and I hope all is well.
Firstly remember that Chimera and ChimeraX are two different programs. Which one are you actually using? We use this address for ChimeraX questions and the other address chimera-users@cgl.ucsf.edu for Chimera questions. So you may want to use the latter in the future if you are really asking about Chimera.
For both programs: You were almost there... if you already have axes defined, you can simply choose both rows in the Axes/Planes/Centroids dialog and the distance and angle will be reported. I.e. in ChimeraX click the row for one axis, then Cmd- (if Mac) or Ctrl-click the row for the other axis.
For a command, ChimeraX is different than Chimera. In Chimera it would just be "angle a1 a2" whereas ChimeraX does not assign those IDs like a1 and a2... instead it uses the model numbers, e.g. ChimeraX commands:
open 2gbp define axis perhelix true angle #1.2.5 #1.2.6
You would look in the Models list (may need to use disclosure triangle to expand to show submodels) to find out the model numbers.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2024, at 8:11 AM, GOVAERTS Cédric via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Ellen
It's me again. still all the way from Belgium .. well happy new year !
I have a Chimera question for which I could not find the answer online. I want to measure the angle between 2 helices (in fact the angle between the first half and the second half of a kinked helix. I know I can define axes for each of the helices halves (giving a1 and a2), but is there a simple way to ask for computing the angles between a1 and a2
Thanks !!
Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgovae rtslab.ulb.ac.be%2F&data=05%7C02%7CCedric.Govaerts%40ulb.be%7Cbe30bcdf 27984a90949b08dc1910bc27%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C 638412806890582302%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjo iV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KWJQHtO8 wqM2t2fI6pereU1DULxhwB%2FaibhauFr0PSo%3D&reserved=0