[3dem] 3D FSC server

[Dmitry Lyumkis]

Thanks, Basil for bringing this to our attention… and to Yong Zi for beating me to the punch!

I have just tested it with a box size of 512, and it works fine, but it will take ~90 minutes. Box sizes of 256 should run over ~4 minutes.

There’s also a standalone version that’s also available, which has a few recent bug-fixes:

https://github.com/LyumkisLab/3DFSC

We have a comprehensive protocol for running the program and evaluating / interpreting the results, which is just awaiting approval by the publisher. For those who are interested, please PM me directly, and I would happy to share it. Hopefully it will help, especially if you’re a new user.

Dmitry


Dmitry Lyumkis
Assistant Professor
The Salk Institute for Biological Studies
10010 North Torrey Pines Road, La Jolla, CA 92037
T: 858-453-4100 x1155
E: dlyumkis at salk.edu<mailto:dlyumkis at salk.edu>
https://lyumkis.salk.edu






On Feb 19, 2020, at 3:34 PM, Basil Greber <basilgreber at gmx.net<mailto:basilgreber at gmx.net>> wrote:

Great, thank you so much! Yes, the results files are fine.

Thanks!

Basil



Am 19.02.2020 um 15:21 schrieb Yong Zi Tan <ytan at nysbc.org<mailto:ytan at nysbc.org>>:

Dear Basil,

I brought the server back-up, and it has started processing all the backlogged jobs. Your job seems to have completed successfully. Do you mind checking if your results are fine? I won't be able to do so as user results are password protected. Thank you!

Warmest Regards,
Yong Zi Tan

-----Original Message-----
From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Yong Zi Tan
Sent: Wednesday, 19 February 2020 6:12 PM
To: Basil Greber; 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] 3D FSC server

Dear Basil,

Thanks for pointing this out - I just checked the server logs and it has been failing since last week. I am on it now and will let you know when it is back up. Thank you!

Warmest Regards,
Yong Zi Tan

-----Original Message-----
From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Basil Greber
Sent: Wednesday, 19 February 2020 5:28 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: [3dem] 3D FSC server

Dear list,

I have used the 3D FSC server previously (and found it to be very useful), but upon attempting to do so yesterday, I got no results. The job status is „DONE“ (not „SUCCESS“) and where the link to the compressed results usually appears, it also says „DONE“ (no link). No images of FSCs are displayed on the results page. Has anyone else had similar issues? Otherwise there may be a problem with my data, though I tried to re-run an old job and that returned the same problem. Any insight would be appreciated.

Thank you, and best regards,

Basil
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