Hi,
I am trying to reproduce the the results from this paper 'Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps', but when I try to run the script from the paper (de3mo) i'm getting the following error:
File: src/utility/options/OptionCollection.cc:1467
Option matching -in:file:override_database_params not found in command line top-level context
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS
I have installed the last version of Rosetta available for download - 2022.49 released on March 19, 2023,
In the paper is mentioned that it should work using weekly releases after February 5, 2023 (version 2023.6 or later) but when I tried to download this version i'm getting the folowing error
Not Found
The requested URL /downloads/academic/2023/wk6 was not found on this server.
Apache/2.2.15 (Red Hat) Server at www.rosettacommons.org Port 443
Any help making this work is higly apreciated.
Thank you.
Sorry about that. There was a slight misconfiguration on the server. I think it should be fixed now.
Please try again.
Hi rmoretti,
Thank you for the promt response.
I downloaded and installed the last version of rosetta (340 from 29 March) but i'm getting the same error when i try to run the script.
Best wishes,
Seba
Looks like there's a bit of a time shift there. While the 2023.6 release is listed as "March 29, 2023", that looks like it's the day it was put up on the website. (Note the 2023.3, 2023.4 and 2023.6 releases all having the same date.) The actual code itself corresponds to Feb 11, 2023. (Which corresponds to Julian week 6) -- you can see that in the tracer output line you get if you just rosetta_scripts without any parameters.
Digging into it, it looks like what you need is release with a code date of 2023-03-15 or later, which is likely to be the 2023.12 weekly (or later), which would be labeled as "r343". -- I'm not sure why the paper implies that the 2023.06 release would work, as it doesn't have some of the features that are needed to run the demo.
Those later weeklies haven't been posted yet, though I'm not quite sure why.
Thank you for looking into it. I will keep an eye for newer versions. Have any ideea when new weeklies will be posted?
Hi,
Any news when the next weekly build that can run this method will be release?
Thank you.
Weekly release 2023.26 is now available for download, and it should contain the updates for the EMERALD paper.