[Chimera-users] Unable to find the angle between planes

[Elaine Meng]

Hi Prathvi,
Please send chimera questions to chimera-users at cgl.ucsf.edu instead of my individual address.  Otherwise, your question may fall through the cracks and not get any answers.

This all works fine for me in Chimera 1.16 release, e.g. commands:

open 5fzp
define plane :252.B & aromatic ring
define plane :261.B & aromatic ring
angle p1 p2

...then the Reply Log contains:

0, chain A: DAIP
#0, chain B: DAIP
5fzp opened
plane name, ID, center, normal, radius: plane: p1 ( 46.248,  56.206,  31.842) ( 0.547, -0.816,  0.186) 1.399
plane name, ID, center, normal, radius: plane: p2 ( 46.861,  61.257,  27.361) ( 0.280,  0.020, -0.960) 1.403
Angle between p1 and p2 is 87.643

I don't know which part you did wrong.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 7, 2023, at 5:23 AM, Prathvi Singh <prathvi at iitk.ac.in> wrote:
> 
> I was using chimera 1.15rc 4 bit but I now installed chimera 1.16 64 bit. I am still getting the mangled atom specifier error.
> 
> On Thu, Jan 5, 2023 at 10:04 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 
> > On Jan 5, 2023, at 12:28 AM, Prathvi Singh <prathvi at iitk.ac.in> wrote:
> > 
> > Hi Elaine,
> > 
> > I am defining two separate planes for the aromatic carbon atoms of TYR252.B & TYR261.B in PDB ID:5FZP.
> > To find the angle between the two planes, I am using the command: angle p1 p2 
> > However, I am getting the error: mangled atom specifier
> > 
> > I followed this thread: https://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012404.html
> > Here you mentioned that angle between two planes can be found using the same command mentioned above. However, it is not working in my case. Please help. 
> > -- 
> > Prathvi Singh,
> > Research Fellow,
> > Department of Biological Sciences & Bioengineering,
> > Indian Institute of Technology, Kanpur-208016
> 
> Hi Prathvi,
> Please clarify which program you are using, or be sure to send Chimera questions to chimera-users at cgl.ucsf.edu and ChimeraX questions to chimerax-users at cgl.ucsf.edu.  If you are using ChimeraX then you cannot specify the plane by something like p1 but instead you need the model number. In Chimera, that command works fine for me.
> Best,
> Elaine
> 
> 
> 
> 
> -- 
> Prathvi Singh,
> Research Fellow,
> Department of Biological Sciences & Bioengineering,
> Indian Institute of Technology, Kanpur-208016