Dear ChimeraX community, I stumbled upon a link<https://www.cgl.ucsf.edu/chimera/data/downloads/1.2470/docs/ContributedSoftw...> discussing a Fourier Transform tool in Chimera. However, I encountered an issue while trying to locate it in my Chimera version (running the command "start Fourier Transform" resulted in an error). My objective is to generate a Fourier space diffraction pattern of a helical reconstructed volume by performing its Fourier transform. I am curious to know if this functionality is available in either Chimera or ChimeraX. Could you kindly provide some guidance on this matter? Thank you in advance for any advice. Abhi
Dear Abhi, In ChimeraX, ...see command "volume fourier" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#fourier> ...which is the same as in the Map Filter tool (in menu under Tools... Volume Data). There are lots of filter types and Fourier Transform is one of them. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapfilter.html> **However, please note that you need to get a recent ChimeraX daily build to have the Map Filter tool. The production release (version 1.6) does not have this tool, only the older command. I can tell this from the Change Log which says when features were added: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2023, at 9:13 AM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX community,
I stumbled upon a link discussing a Fourier Transform tool in Chimera. However, I encountered an issue while trying to locate it in my Chimera version (running the command "start Fourier Transform" resulted in an error). My objective is to generate a Fourier space diffraction pattern of a helical reconstructed volume by performing its Fourier transform. I am curious to know if this functionality is available in either Chimera or ChimeraX. Could you kindly provide some guidance on this matter?
Thank you in advance for any advice. Abhi
Keep in mind that the ChimeraX Fourier transform just gives
On Jun 30, 2023, at 9:33 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Abhi, In ChimeraX,
...see command "volume fourier" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#fourier>
...which is the same as in the Map Filter tool (in menu under Tools... Volume Data). There are lots of filter types and Fourier Transform is one of them. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapfilter.html>
**However, please note that you need to get a recent ChimeraX daily build to have the Map Filter tool. The production release (version 1.6) does not have this tool, only the older command. I can tell this from the Change Log which says when features were added: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2023, at 9:13 AM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX community,
I stumbled upon a link discussing a Fourier Transform tool in Chimera. However, I encountered an issue while trying to locate it in my Chimera version (running the command "start Fourier Transform" resulted in an error). My objective is to generate a Fourier space diffraction pattern of a helical reconstructed volume by performing its Fourier transform. I am curious to know if this functionality is available in either Chimera or ChimeraX. Could you kindly provide some guidance on this matter?
Thank you in advance for any advice. Abhi
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Abhi, The ChimeraX Fourier transform capability has limited utility since ChimeraX has not capabilities aimed and analyzing Fourier space maps. ChimeraX doesn't handle complex value maps, so the volume fourier command just gives the Fourier coefficient magnitudes, although there is an option to get the phases, but then you have two scalar maps and not tools to work with them within ChimeraX. Tom
On Jun 30, 2023, at 11:08 AM, Tom Goddard <goddard@sonic.net> wrote:
Keep in mind that the ChimeraX Fourier transform just gives
On Jun 30, 2023, at 9:33 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Abhi, In ChimeraX,
...see command "volume fourier" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#fourier>
...which is the same as in the Map Filter tool (in menu under Tools... Volume Data). There are lots of filter types and Fourier Transform is one of them. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapfilter.html>
**However, please note that you need to get a recent ChimeraX daily build to have the Map Filter tool. The production release (version 1.6) does not have this tool, only the older command. I can tell this from the Change Log which says when features were added: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2023, at 9:13 AM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX community,
I stumbled upon a link discussing a Fourier Transform tool in Chimera. However, I encountered an issue while trying to locate it in my Chimera version (running the command "start Fourier Transform" resulted in an error). My objective is to generate a Fourier space diffraction pattern of a helical reconstructed volume by performing its Fourier transform. I am curious to know if this functionality is available in either Chimera or ChimeraX. Could you kindly provide some guidance on this matter?
Thank you in advance for any advice. Abhi
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Thank you! ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: 30 June 2023 14:12 To: Das, Abhinaba <abhinaba.das@emory.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [External] Re: [chimerax-users] Fourier transform tool in chimeraX? Hi Abhi, The ChimeraX Fourier transform capability has limited utility since ChimeraX has not capabilities aimed and analyzing Fourier space maps. ChimeraX doesn't handle complex value maps, so the volume fourier command just gives the Fourier coefficient magnitudes, although there is an option to get the phases, but then you have two scalar maps and not tools to work with them within ChimeraX. Tom
On Jun 30, 2023, at 11:08 AM, Tom Goddard <goddard@sonic.net> wrote:
Keep in mind that the ChimeraX Fourier transform just gives
On Jun 30, 2023, at 9:33 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Abhi, In ChimeraX,
...which is the same as in the Map Filter tool (in menu under Tools... Volume Data). There are lots of filter types and Fourier Transform is one of them. <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmapfilter.html&data=05%7C01%7Cabhinaba.das%40emory.edu%7Cf98a4858e22545ad1d6108db79958aec%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638237455420004431%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=oe1K3f%2FNPgAvYNAUzWxEfpFsxiswbPeOBZnCTrMVfZU%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapfilter.html>>
**However, please note that you need to get a recent ChimeraX daily build to have the Map Filter tool. The production release (version 1.6) does not have this tool, only the older command. I can tell this from the Change Log which says when features were added: <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fwiki%2FChangeLog&data=05%7C01%7Cabhinaba.das%40emory.edu%7Cf98a4858e22545ad1d6108db79958aec%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638237455420004431%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1u3r2GVFV3vM1y6PqcYvLGSpqvSgxa%2F9mEyuZaVo2%2BE%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2023, at 9:13 AM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX community,
I stumbled upon a link discussing a Fourier Transform tool in Chimera. However, I encountered an issue while trying to locate it in my Chimera version (running the command "start Fourier Transform" resulted in an error). My objective is to generate a Fourier space diffraction pattern of a helical reconstructed volume by performing its Fourier transform. I am curious to know if this functionality is available in either Chimera or ChimeraX. Could you kindly provide some guidance on this matter?
Thank you in advance for any advice. Abhi
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
participants (3)
-
Das, Abhinaba -
Elaine Meng -
Tom Goddard