[Chimera-users] imod

Tue Jul 12 23:17:33 PDT 2022

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 at cam.ac.uk<mailto:Av623 at cam.ac.uk>

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From: Elaine Meng<mailto:meng at cgl.ucsf.edu>
Sent: 12 July 2022 17:07
To: Aaran Vijayakumaran<mailto:av623 at mrc-tox.cam.ac.uk>
Cc: chimera-users at cgl.ucsf.edu<mailto:chimera-users at 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 at 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 at cam.ac.uk

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