[3dem] GMS3.5 shutdown experiences

Nilakshee Bhattacharya, Ph.D. nilakshee.bhattacharya at duke.edu
Fri Apr 8 06:58:26 PDT 2022

Dear Marcus,

We have a K3 on a Krios at Duke. I upgraded the GMS version to a 3.5 and recently to 3.5.1. Along with our 3.5 version upgrade, I also upgraded our SerialEM software to be compatible. Our Duke users collect SPA data using latitude and version 3.5 had the image shift option by which we could collect many targets for each focus. Version 3.5.1 is said to have a better comma correction.

With the version upgrades as per our experience the K3 has been more stable with occasional crashes. The syncing has been much better too. We did go through all the upgrades and don't think skipped any. Maybe something simple like a reinstalling might help.


Nilakshee Bhattacharya, PhD
CryoEM Manager
Shared Materials Instrumentation Facility (SMIF)
101 Science Dr.
Duke University, Durham, NC 27708-0271

From: 3dem <3dem-bounces at ncmir.ucsd.edu> On Behalf Of Marcus FISLAGE
Sent: Friday, April 8, 2022 8:28 AM
To: Reinhard Rachel <Reinhard.Rachel at biologie.uni-regensburg.de>; 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] GMS3.5 shutdown experiences

Hi Reinhard and others,

first, please note that I upgraded from version 3.3 and skipped the 3.4.  So, my reasons may not apply to you.

The reasoning for my upgrade is not because of features per se but more because of stability and constant errors from the old software/firmware combination. The upgrade was not directly advised by David or Gatan, but also not discouraged.
With the 3.3 version we had to regularly restart the Camera fully because of several syncing errors. The initial advise of Gatan was just to restart the PC, but often the restart still resulted in a bad sync and bad 'health status'. This needed to be sometimes done twice or thrice in a row. A shutdown PC and restart PC was more successful but was rather annoying because somebody needs to come in to physically push the button. But in many cases that was still not enough, and we needed to cycle the Power supply of the K3 as well, which leads to even longer delays before we could restart the data collection. (This whole issue does not exist anymore, except of this major new type of problem)
The other main reason was that the K3 was always rather bad at interpolating the gain reference if some images were done with a significant lower beam intensity than the gain. This was a nuisance if we had samples where we measured in significantly different ice thicknesses. Our engineer indicated that this behavior may be improved in the latest version. (Not sure it is that much different (yet).)

We knew from a recent install close by here on a JEOL2100 w. SerialEM that came directly with GMS3.5 that the software itself works so I wanted to give it a try to see if it alleviates most of my camera sync errors. But note they are just doing performance test, so they do not (yet) collect thousands of imaged per day.

A feature that I came by that is different is that the camera uses different suggested reference intensities now as well for CDS and non-CDS mode when doing the linear reference. In 3.3 it only distinguished in counting mode. However, this will probably not really matter.

I of course would like to know how common this new issue is and to what extent it may be a Gatan-JEOL, Gatan-SerialEM or pure Gatan issue. My money is currently completely on the latter option. And if my regular restart quick fix of GMS3.5 works I still majorly prefer it over my issues with GMS3.3.



Please note upcoming days with limited access to BECM:

22 April - 2nd May

Dr. Marcus Fislage

EM Manager

VIB-Center for Structural Biology
VUB (Vrije Universiteit Brussel)
Building P1T, room 0.01
Pleinlaan 2

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.becm.be&d=DwIFAw&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=MPAlRygzgRhFKRiVCRGc9yuxAGXzZsC525UXAsIYoSaK81z7rPA0DIl06s_d7YFA&s=VUIFkcV1gcGSNxW42ngc0xNdRDiiOkpdRP83xDUKMfc&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.becm.be&d=DwMFAw&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=FkJH7Kb7Y-tEZ7ekkMmrh8yZ8Hxbwnsx8kSn21ERWeTqFtM38aWSaN2ALYOEoupW&s=8vKP9fKScNm9e7DXLPFePd98aej-ZRGSOHztOXdGcy4&e=>

From: Reinhard Rachel <Reinhard.Rachel at biologie.uni-regensburg.de<mailto:Reinhard.Rachel at biologie.uni-regensburg.de>>
Sent: Friday, April 8, 2022 12:06 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>; Marcus FISLAGE <Marcus.Fislage at vub.be<mailto:Marcus.Fislage at vub.be>>
Subject: Re: GMS3.5 shutdown experiences

> Dear all,
> since we upgraded our Camera software from Gatan to version 3.5 (K3 camera
> on JEOL CryoARM300 using SerialEM 4.0.1-4) we experienced regular full
> shutdowns of the GMS software. I.e. no error message and the whole software

> package is just not running anymore. And a simple reopening of the GMS3
> software works and I can continue the data collection.
> I am already in contact with our Gatan engineer, but he is rather surprised

> about this behavior.
> I would therefore like to ask the crowd if you have had or currently have a

> similar experience.
> To the best of my knowledge, it appears that the frequency of GMS shutdown
> is correlated to the number of images taken. I.e. After a certain threshold

> of images taken with the K3 camera, the GMS software will just disappear.
> I currently tested it by a daily (or every second day) restart of the GMS
> software and since then the error did not appear again for 2 weeks. This
> would initially support my theory.

valuable to know, Marcus.
question back to you:
is there any good reason to upgrade GMS to 3.5?
any interesting features I am not aware of?
is this version "better" in any aspect?
or just recommended by -a- Gatan, or by -b- David M?
thank you and kind regards,

Prof. Dr. Reinhard Rachel
University of Regensburg
Centre for EM / Anatomy
Faculty of Biology & Preclin. Med.
Universitaetsstrasse 31
D-93053 Regensburg - Germany
tel +49 941 943 -2837, -1666
mail reinhard.rachel at biologie.uni-regensburg.de<mailto:reinhard.rachel at biologie.uni-regensburg.de>
office: VKL 3.1.29
member of the IFSM board

Next microscopy conferences:
- MC2023, DGE: 26.2.-2.3. 2023
- next European EM conf.: EMC2024 in Kopenhagen, August 2024
- IMC20 in Busan, South Korea: Sept, 2023
- next Microbiol. conferences:  VAAM 26.2.-1.3. 2023 - Göttingen
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