Re: [Chimera-users] Unable to find the angle between planes
Hi Prathvi, Please send chimera questions to chimera-users@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@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@cgl.ucsf.edu> wrote:
On Jan 5, 2023, at 12:28 AM, Prathvi Singh <prathvi@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@cgl.ucsf.edu and ChimeraX questions to chimerax-users@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
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@cgl.ucsf.edu> wrote:
Hi Prathvi, Please send chimera questions to chimera-users@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@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@cgl.ucsf.edu> wrote:
On Jan 5, 2023, at 12:28 AM, Prathvi Singh <prathvi@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@cgl.ucsf.edu and ChimeraX questions to chimerax-users@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
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Prathvi Singh