[3dem] 3dem Digest, Vol 155, Issue 19

[Zhao, Haiyan]

I got a protein complex structure including 26 subunits and molecular weight 1MDa  with overall resolution at 4.0A, after local resolution calculation, some parts even are close to 3.5A, but one part goes to 15A, I tried to use multibody refinement in the Relion,  I only can give two bodies (due computer limit). After multibody refinement, resolution can improve to 6A, I tried focus refinement, it is not working, I wonder what difference between multibody refinement  ( two bodies ) and focus refinement?
Do you have a detail tutorial for focus refinement?
For focus refinement, after i did multibody refinement, I did particle subtraction, then do 3D auto-refinement with subtraction particles, the command like:
`which relion_refine_mpi` --o Refine3D/job084/run --auto_refine --split_random_halves --i Subtract/job068/subtracted.star --ref MultiBody/job056/run_body001.mrc --ini_high 15 --dont_combine_weights_via_disc --no_parallel_disc_io --pool 10 --pad 1  --skip_gridding  --ctf --ctf_corrected_ref --particle_diameter 200 --flatten_solvent --zero_mask --solvent_mask MultiBody/job056/run_body001_mask.mrc --solvent_correct_fsc  --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale  --j 2 --gpu ""  --pipeline_control Refine3D/job084/
The focus refinement result is worse than multibody refinement.
Any input?

Haiyan Zhao

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Subject: 3dem Digest, Vol 155, Issue 19

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Today's Topics:

   1. Re: Tools for Sample Prep & Loading (Jean-Philippe Demers, Mr)


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Message: 1
Date: Sat, 11 Jul 2020 08:26:58 +0000
From: "Jean-Philippe Demers, Mr" <jean-philippe.demers at mail.mcgill.ca>
To: Michael Godfrin <mgodfrin at nanosoftmaterials.com>,
        "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Tools for Sample Prep & Loading
Message-ID:
        <YQBPR0101MB0785746EC721C773454FDD78EB620 at YQBPR0101MB0785.CANPRD01.PROD.OUTLOOK.COM>

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________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Michael Godfrin <mgodfrin at nanosoftmaterials.com>
Sent: Friday, July 10, 2020 5:16:07 AM
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: [3dem] Tools for Sample Prep & Loading

Hello Everyone,

We are now offering the Autogrid Tweezers<https://urldefense.com/v3/__https://www.nanosoftmaterials.com/autogrid-tweezer__;!!Mih3wA!WQP7K2_-M6BGn68iB-5ASXdMjh6jdrFdMs2AE50loTgYcz9-lwoh-0coGkNfYb_gmQ$> that are used to handle autogrids/cartridges and load them into the autoloader cassette.  Our version performs the same as the Thermo Fisher Scientific version (same critical geometries), while we offer them at a much lower price, so they are a great option for replacement of damaged Autogrid Tweezers or to build up a rotation of them for the workflow.

We are also offering the metal components<https://urldefense.com/v3/__https://www.nanosoftmaterials.com/vitrobotdewarparts__;!!Mih3wA!WQP7K2_-M6BGn68iB-5ASXdMjh6jdrFdMs2AE50loTgYcz9-lwoh-0coGkNX7tbQuQ$> of the Vitrobot dewar.  Each of the metal parts performs equally to the Thermo Fisher version, and are offered at a lower price (we have found even comparable to university machine shop pricing) so can replace lost or damaged parts or also be used for custom plunge systems.

Have a nice weekend!
Mike


Michael Godfrin, PhD
President

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https://urldefense.com/v3/__http://www.nanosoftmaterials.com__;!!Mih3wA!UbSXMSqzA9FXJvGs8L1OHcN7gyTrob1oZYyju_81EE2WUUONyHakHQEDppF3p0hHNw$ <https://urldefense.com/v3/__http://www.nanosoftmaterials.com__;!!Mih3wA!WQP7K2_-M6BGn68iB-5ASXdMjh6jdrFdMs2AE50loTgYcz9-lwoh-0coGkPVjy6e8A$>

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