Dear all, I was wondering if it was possible to measure the distance of structures within an IMOD segmentation file. For instance, measuring the length of microtubules lets say? Thank you in advance for any assistance. Bests, Aaran Vijayakumaran PhD Researcher Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623@cam.ac.uk<mailto:Av623@cam.ac.uk> [A picture containing text, screenshot Description automatically generated] [cid:image001.png@01D84DAF.64335190]
Hi Aaran, You may want to use ChimeraX instead of Chimera: ChimeraX has a "mouse mode" (e.g. can be assigned to right mouse button) called "tape measure" where you can click and drag out a measurement. You can assign it to the right mouse button by going to the icon toolbar across the top of the ChimeraX window, and in the Right Mouse tab, clicking the icon that looks like a tape measure: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tape> Actually I am not 100% sure it works on IMOD surfaces and I don't have an example to try, but it works on both map isosurfaces and molecular surfaces. In Chimera, I believe the way to do it is to put markers (which are essentially fake atoms) on the IMOD surface where you want to measure to/from and then measure the marker-marker distance (essentially it's the same as how to measure an atom-atom distance). In Chimera you can add markers with Volume Tracer: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html> ...and then Ctrl-click one marker, Shift-Ctrl-click the second marker and use context menu to "Show Distance" as mentioned here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#contextmenus> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances> ChimeraX also has markers and atom-atom distance measurements, but that approach is more steps than using its "tape measure" mouse mode. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2022, at 5:02 AM, Aaran Vijayakumaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, I was wondering if it was possible to measure the distance of structures within an IMOD segmentation file. For instance, measuring the length of microtubules lets say?
Thank you in advance for any assistance. Bests,
Aaran Vijayakumaran PhD Researcher Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623@cam.ac.uk
Hi, Thank you. I seem to receive an error when downloading ChimeraX with regards to the setup – never come across something like this before so confused. BW Aaran Vijayakumaran PhD Researcher (Mennella lab) Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623@cam.ac.uk<mailto:Av623@cam.ac.uk> [A picture containing text, screenshot Description automatically generated] [cid:image001.png@01D84DAF.64335190] From: Elaine Meng<mailto:meng@cgl.ucsf.edu> Sent: 12 July 2022 17:07 To: Aaran Vijayakumaran<mailto:av623@mrc-tox.cam.ac.uk> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] imod Hi Aaran, You may want to use ChimeraX instead of Chimera: ChimeraX has a "mouse mode" (e.g. can be assigned to right mouse button) called "tape measure" where you can click and drag out a measurement. You can assign it to the right mouse button by going to the icon toolbar across the top of the ChimeraX window, and in the Right Mouse tab, clicking the icon that looks like a tape measure: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmousemodes.html%23tape&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1vlMeHD3433WTHiJEiLC%2Bw6uA1LmCkJ7bGMc027QVIQ%3D&reserved=0> Actually I am not 100% sure it works on IMOD surfaces and I don't have an example to try, but it works on both map isosurfaces and molecular surfaces. In Chimera, I believe the way to do it is to put markers (which are essentially fake atoms) on the IMOD surface where you want to measure to/from and then measure the marker-marker distance (essentially it's the same as how to measure an atom-atom distance). In Chimera you can add markers with Volume Tracer: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumepathtracer%2Fframevolpath.html&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4x%2F0t4DZDWP3OuTZEw4VGY%2BrtDNLmq3cbEFV%2BKJ4viE%3D&reserved=0> ...and then Ctrl-click one marker, Shift-Ctrl-click the second marker and use context menu to "Show Distance" as mentioned here: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmouse.html%23contextmenus&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=6BsqQ0K4jfxO1%2BwK9BXDsqDSA2TfURjMROAETLgiLns%3D&reserved=0> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fstructuremeas%2Fstructuremeas.html%23distances&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vtBqLoPgt3HYhS9ikG2uyTDPad19ZK2GD%2Fmpg%2FbYfHw%3D&reserved=0> ChimeraX also has markers and atom-atom distance measurements, but that approach is more steps than using its "tape measure" mouse mode. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2022, at 5:02 AM, Aaran Vijayakumaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, I was wondering if it was possible to measure the distance of structures within an IMOD segmentation file. For instance, measuring the length of microtubules lets say?
Thank you in advance for any assistance. Bests,
Aaran Vijayakumaran PhD Researcher Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623@cam.ac.uk
Hi Aaran, You can use the markers approach I described in Chimera if you don't want to use ChimeraX. If you want to use ChimeraX, we would need more details as to the problem you had, e.g. what steps you did and what error occurred. This chimera-users mailing list is for Chimera, but there are other address(es) recommended if you have questions specifically about ChimeraX, see: <https://rbvi.ucsf.edu/chimerax/docs/contact.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 Jul 12, 2022, at 11:17 PM, Aaran Vijayakumaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
Thank you. I seem to receive an error when downloading ChimeraX with regards to the setup – never come across something like this before so confused. BW
Aaran Vijayakumaran PhD Researcher (Mennella lab) Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623@cam.ac.uk
<28CD0EC75E694D1B956F1D2A4867BDC9[2020242].png>
<B9080D6EAC89480FB83F84D776C7B591[2020243].png>
From: Elaine Meng Sent: 12 July 2022 17:07 To: Aaran Vijayakumaran Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] imod
Hi Aaran, You may want to use ChimeraX instead of Chimera: ChimeraX has a "mouse mode" (e.g. can be assigned to right mouse button) called "tape measure" where you can click and drag out a measurement. You can assign it to the right mouse button by going to the icon toolbar across the top of the ChimeraX window, and in the Right Mouse tab, clicking the icon that looks like a tape measure: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmousemodes.html%23tape&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1vlMeHD3433WTHiJEiLC%2Bw6uA1LmCkJ7bGMc027QVIQ%3D&reserved=0>
Actually I am not 100% sure it works on IMOD surfaces and I don't have an example to try, but it works on both map isosurfaces and molecular surfaces.
In Chimera, I believe the way to do it is to put markers (which are essentially fake atoms) on the IMOD surface where you want to measure to/from and then measure the marker-marker distance (essentially it's the same as how to measure an atom-atom distance). In Chimera you can add markers with Volume Tracer: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumepathtracer%2Fframevolpath.html&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4x%2F0t4DZDWP3OuTZEw4VGY%2BrtDNLmq3cbEFV%2BKJ4viE%3D&reserved=0>
...and then Ctrl-click one marker, Shift-Ctrl-click the second marker and use context menu to "Show Distance" as mentioned here: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmouse.html%23contextmenus&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=6BsqQ0K4jfxO1%2BwK9BXDsqDSA2TfURjMROAETLgiLns%3D&reserved=0> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fstructuremeas%2Fstructuremeas.html%23distances&data=05%7C01%7Cav623%40mrc-tox.cam.ac.uk%7C61e918e69037451fb0cb08da6420a672%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637932388642915480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vtBqLoPgt3HYhS9ikG2uyTDPad19ZK2GD%2Fmpg%2FbYfHw%3D&reserved=0>
ChimeraX also has markers and atom-atom distance measurements, but that approach is more steps than using its "tape measure" mouse mode.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2022, at 5:02 AM, Aaran Vijayakumaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, I was wondering if it was possible to measure the distance of structures within an IMOD segmentation file. For instance, measuring the length of microtubules lets say?
Thank you in advance for any assistance. Bests,
Aaran Vijayakumaran PhD Researcher Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623@cam.ac.uk
participants (2)
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Aaran Vijayakumaran -
Elaine Meng