[3dem] 3dem Digest, Vol 174, Issue 38
John Monroe Heumann
john.heumann at colorado.edu
Mon Feb 28 12:12:28 PST 2022
Hi Joanna!
First, please update to a more recent version of IMOD (4.11.x or 4.12.x).
There have been lots of enhancements and bug fixes (including 3D CTF),
which will let you get better results. Regarding your other 2 questions,
IMOD routinely reconstructs tomograms in this unusual orientation; things
get restored to the standard configuration during the final post-processing
step, typically by rotating about x (which effectively interchanges the y
and z axis but without flipping handedness).
Best,
-jh-
On Mon, Feb 28, 2022 at 1:00 PM <3dem-request at ncmir.ucsd.edu> wrote:
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> Today's Topics:
>
> 1. Reconstructing a K3 tomogram (Joanna Brown)
> 2. Re: Reconstructing a K3 tomogram (Ludtke, Steven J.)
> 3. Cryo-EM Core Facility Manager Position at Weill Cornell
> Medicine (Joel Meyerson)
>
>
>
> ---------- Forwarded message ----------
> From: Joanna Brown <joanna.brown at astx.com>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Cc:
> Bcc:
> Date: Mon, 28 Feb 2022 15:33:41 +0000
> Subject: [3dem] Reconstructing a K3 tomogram
>
> Hello everyone,
>
>
>
> I’m looking for some help reconstructing a tomogram taken on a Krios with
> a K3 detector.
>
>
>
> I’m doing the reconstruction with imod/etomo v4.9. I’ve taken a relatively
> low mag tomogram of a 0.6/1 quantifoil hole with particles in it so I can
> see the particle distribution and ice thickness. I can see the whole
> foilhole in the field of view.
>
>
>
> I am using patch tracking and everything looks fine with the aligned
> stacks until I come to the point in the process where a tomogram needs to
> be computed, including making the sample tomogram to generate the boundary
> model. (At least I think it does, but I have to admit, I’m pretty rusty
> with imod/etomo!)
>
>
>
> I notice that the X and the Z axis seem to become switched and I end up
> with a tomogram of over 1500 Z slices that corresponds to the pixel
> dimensions of the K3 detector. The reconstruction also becomes very
> strange, the protein particles (these look reasonable though strangely
> arranged relative to each other) visible in a separate plane from the foil
> hole, which ends up looking like an eye shape instead of a round hole. I
> tried to compute the tomogram using WBP.
>
>
>
> Thoughts I have had to try to fix problem are:
>
>
>
> 1. Try making an initial X,Y boundary model to only include the foil
> hole for patch tracking and exclude all the carbon and very small
> particles.
> 2. Try a low pass filter?
> 3. No idea what to do about the swapping of X and Z dimensions – help!
>
>
>
> Any suggestions or pointing out my obvious glaring error/stupidity totally
> welcome!
>
>
>
> Thanks so much!
>
>
>
> Joanna Brown
>
>
>
>
>
>
>
>
> This email and any attachments thereto may contain private, confidential,
> and privileged material for the sole use of the intended recipient. Any
> review, copying or distribution of this email (or any attachments thereto)
> by others is strictly prohibited. If you are not the intended recipient,
> please delete the original and any copies of this email and any attachments
> thereto and notify the sender immediately.
>
>
>
> ---------- Forwarded message ----------
> From: "Ludtke, Steven J." <sludtke at bcm.edu>
> To: Joanna Brown <joanna.brown at astx.com>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Bcc:
> Date: Mon, 28 Feb 2022 15:42:28 +0000
> Subject: Re: [3dem] Reconstructing a K3 tomogram
> Hi Joanna,
> while I'm sure there are IMOD solutions to this problem, you might
> consider trying:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__eman2.org_e2TomoSmall&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=hkBsAbmjFsuOl3AfY53ewWHrJOk-eJysAKmG3GjQEAJzkRcMu_mOnjgPmHUwT_Ea&s=h42rNc16Ox6HW6Mi1vT0MrwLZhCYRgwD9_Ev2q4miko&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__eman2.org_e2TomoSmall&d=DwMGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=6N7sfHZaBpcerWmtN1_-l1d04aKUt54QeF2j5nE49l3TFxgEzKxiLQEVD_BL4zB2&s=MwUubCDvPDj6bqvz73Cdcv689W8nOTEYvmhTiLGYM48&e=>
>
> which is fully automated and will produce downsampled tomograms by
> default, but return to the fully sampled data if you extract local regions
> (for example for subtomogram averaging).
>
>
> --------------------------------------------------------------------------------------
> Steven Ludtke, Ph.D. <sludtke at bcm.edu> Baylor
> College of Medicine
> Charles C. Bell Jr., Professor of Structural Biology
> Dept. of Biochemistry and Molecular Biology (
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_biochem&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=hkBsAbmjFsuOl3AfY53ewWHrJOk-eJysAKmG3GjQEAJzkRcMu_mOnjgPmHUwT_Ea&s=ZXg_Y3OWDDHqWS-1ogd4JiCOAjQr2OlrZdP0AzcIjI8&e=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_biochem&d=DwMGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=6N7sfHZaBpcerWmtN1_-l1d04aKUt54QeF2j5nE49l3TFxgEzKxiLQEVD_BL4zB2&s=7oxCscH0XQv55BzHQ56DytgpGhs5nGDErj49B3U4T50&e=>
> )
> Academic Director, CryoEM Core (
> cryoem.bcm.edu
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__cryoem.bcm.edu&d=DwMGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=6N7sfHZaBpcerWmtN1_-l1d04aKUt54QeF2j5nE49l3TFxgEzKxiLQEVD_BL4zB2&s=c3N_c2MswvfkmffWYmrECnGnp16qPZ76-SmY2EMzlXw&e=>
> )
> Co-Director CIBR Center (
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_research_cibr&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=hkBsAbmjFsuOl3AfY53ewWHrJOk-eJysAKmG3GjQEAJzkRcMu_mOnjgPmHUwT_Ea&s=kijn9ODBPwnAUZTpSY-r5MRLmLreclGwHfkPdJiBlEg&e=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_research_cibr&d=DwMGaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=6N7sfHZaBpcerWmtN1_-l1d04aKUt54QeF2j5nE49l3TFxgEzKxiLQEVD_BL4zB2&s=iU2lOg-ofxPcbKWVV17FmU6Lit5X3tH-ggvKsVWotII&e=>
> )
>
>
>
> On Feb 28, 2022, at 9:33 AM, Joanna Brown <joanna.brown at astx.com> wrote:
>
> ****CAUTION:*** This email is not from a BCM Source. Only click links or
> open attachments you know are safe.*
> ------------------------------
> Hello everyone,
>
> I’m looking for some help reconstructing a tomogram taken on a Krios with
> a K3 detector.
>
> I’m doing the reconstruction with imod/etomo v4.9. I’ve taken a relatively
> low mag tomogram of a 0.6/1 quantifoil hole with particles in it so I can
> see the particle distribution and ice thickness. I can see the whole
> foilhole in the field of view.
>
> I am using patch tracking and everything looks fine with the aligned
> stacks until I come to the point in the process where a tomogram needs to
> be computed, including making the sample tomogram to generate the boundary
> model. (At least I think it does, but I have to admit, I’m pretty rusty
> with imod/etomo!)
>
> I notice that the X and the Z axis seem to become switched and I end up
> with a tomogram of over 1500 Z slices that corresponds to the pixel
> dimensions of the K3 detector. The reconstruction also becomes very
> strange, the protein particles (these look reasonable though strangely
> arranged relative to each other) visible in a separate plane from the foil
> hole, which ends up looking like an eye shape instead of a round hole. I
> tried to compute the tomogram using WBP.
>
> Thoughts I have had to try to fix problem are:
>
>
> 1. Try making an initial X,Y boundary model to only include the foil
> hole for patch tracking and exclude all the carbon and very small particles.
> 2. Try a low pass filter?
> 3. No idea what to do about the swapping of X and Z dimensions – help!
>
>
> Any suggestions or pointing out my obvious glaring error/stupidity totally
> welcome!
>
> Thanks so much!
>
> Joanna Brown
>
>
>
>
> This email and any attachments thereto may contain private, confidential,
> and privileged material for the sole use of the intended recipient. Any
> review, copying or distribution of this email (or any attachments thereto)
> by others is strictly prohibited. If you are not the intended recipient,
> please delete the original and any copies of this email and any attachments
> thereto and notify the sender immediately.
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=C3fzn7jzZWOMI2X9k8ntIbJg7WhCTbbdWWJtHDCAC-zV9f-1jj_gN5c1RiI2oT17&s=lNgOi3yNU9tZGDS903rvQOvy8mVGR5FqK6C8EEhyQ9o&e=
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Joel Meyerson <jrm2008 at med.cornell.edu>
> To: 3dem <3dem at ncmir.ucsd.edu>
> Cc:
> Bcc:
> Date: Mon, 28 Feb 2022 19:59:40 +0000
> Subject: [3dem] Cryo-EM Core Facility Manager Position at Weill Cornell
> Medicine
>
> Weill Cornell Medicine (WCM) in New York City is hiring a Cryo-EM Core
> Facility Manager. The position will involve managing the electron
> microscopy imaging equipment, associated computing infrastructure, and
> peripherals located in the Cryo-EM Core Facility.
>
>
>
> The facility houses a 200 keV Glacios TEM equipped with a Falcon IV
> detector and Selectris energy filter and a Vitrobot IV automated EM grid
> plunge freezer. Data processing is carried out on shared compute nodes
> managed by the WCM Scientific Computing Unit.
>
>
>
> This position offers opportunities for the incumbent to directly
> participate in research on the structure and function of macromolecules
> involved in different biological processes, and interact with other
> scientists at WCM.
>
>
>
> More details about the position and information on how to apply can be
> found at:
>
>
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__career4.successfactors.com_sfcareer_jobreqcareer-3FjobId-3D66908-26company-3DC0000274692P&d=DwIFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=hkBsAbmjFsuOl3AfY53ewWHrJOk-eJysAKmG3GjQEAJzkRcMu_mOnjgPmHUwT_Ea&s=cR2GIKkwk-Lc4ZCiAGJPR9JCVRgrpKdUnt0knCv2RZ0&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__career4.successfactors.com_sfcareer_jobreqcareer-3FjobId-3D66908-26company-3DC0000274692P&d=DwQFAg&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=4mBczXjs2xeH0UELegqXtvJuYbxH3UQTuPiIA-d3Jni1_uL8a2OkoVXYyqTVFttL&s=1zh502loIIgenZJEi0oatv7jg3rW23DyuCPbheYQ0sU&e=>
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