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

[Prathvi Singh]

Apologies for sending it directly to you. I was able to figure out the
problem though. I had created an alias named *angle *due to which whenever
I ran the *angle *command, the alias would run instead of the built-in *angle
*command. I deleted that alias and created a new one with a different name
& now everything is working fine.

Thanks again for your help

On Sun, Jan 8, 2023 at 10:53 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20230111/e1a19208/attachment.html>