calculating orientation parameters between two asymmetric units
Dear All, How can I compute the parameters (angle , shift) of orientation between 2 asymmetric units w.r.t the central axis in a density map (and the map is not helical). Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>
Hi Anindito, If you have a PDB (atomic) structure of which you open two copies, and then fit them into the two asymmetric units of the map, then you could use "measure rotation" to measure the rotation and shift between those two atomic copies. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> If you currently have only the map and not the fitted atomic structures, then you could try "measure symmetry" but it only works on certain cases and I don't know if it would work on yours. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry> If you're interested in maybe switching from Chimera to ChimeraX, ChimeraX also has these measure command options (although syntax may be slightly different). ChimeraX measure: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2022, at 8:42 PM, Sen, Anindito via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear All, How can I compute the parameters (angle , shift) of orientation between 2 asymmetric units w.r.t the central axis in a density map (and the map is not helical).
HI Elaine, what will be a typical command for the job with 2 asymmetric units in Chimera and ChimeraX. I will try both. Thanks for the help. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, February 4, 2022 10:39 AM To: Sen, Anindito <andysen@tamu.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] calculating orientation parameters between two asymmetric units Hi Anindito, If you have a PDB (atomic) structure of which you open two copies, and then fit them into the two asymmetric units of the map, then you could use "measure rotation" to measure the rotation and shift between those two atomic copies. ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hi Anindito, If you have a PDB (atomic) structure of which you open two copies, and then fit them into the two asymmetric units of the map, then you could use "measure rotation" to measure the rotation and shift between those two atomic copies. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... > If you currently have only the map and not the fitted atomic structures, then you could try "measure symmetry" but it only works on certain cases and I don't know if it would work on yours. <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... > If you're interested in maybe switching from Chimera to ChimeraX, ChimeraX also has these measure command options (although syntax may be slightly different). ChimeraX measure: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2022, at 8:42 PM, Sen, Anindito via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear All, How can I compute the parameters (angle , shift) of orientation between 2 asymmetric units w.r.t the central axis in a density map (and the map is not helical).
Hi Anindito, Well if you had two copies of the same atomic structure as models #2,3 already fitted into the two different parts of map #1, then the command could be something like Chimera: measure rotation #2 #3 ChimeraX: measure rotation #2 toModel #3 Or to try to figure it out from map alone, maybe a command something like (same in both programs): measure symmetry #1 However, you should still take a look at the help links I sent before, because you might want or even need to use some of the other command options. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 4, 2022, at 3:44 PM, Sen, Anindito via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
HI Elaine,
what will be a typical command for the job with 2 asymmetric units in Chimera and ChimeraX. I will try both.
Thanks for the help.
Stay safe & Regards
Anindito Sen. Ph.D
Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257
Office: ILSB Room 1133 Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, February 4, 2022 10:39 AM To: Sen, Anindito <andysen@tamu.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] calculating orientation parameters between two asymmetric units
This Message Is From an External Sender This message came from outside your organization. Hi Anindito, If you have a PDB (atomic) structure of which you open two copies, and then fit them into the two asymmetric units of the map, then you could use "measure rotation" to measure the rotation and shift between those two atomic copies. < https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid...
If you currently have only the map and not the fitted atomic structures, then you could try "measure symmetry" but it only works on certain cases and I don't know if it would work on yours. < https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid...
If you're interested in maybe switching from Chimera to ChimeraX, ChimeraX also has these measure command options (although syntax may be slightly different). ChimeraX measure: < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 3, 2022, at 8:42 PM, Sen, Anindito via Chimera-users < chimera-users@cgl.ucsf.edu wrote:
Dear All, How can I compute the parameters (angle , shift) of orientation between 2 asymmetric units w.r.t the central axis in a density map (and the map is not helical).
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Sen, Anindito