Relion has recently updated ver3.1 and its star file changes a lot, and then I found it could not import into cisTEM to run. New star file seems like:
1 opticsGroup0 0.100000 2.700000 300.000000 1.310000 1.310000 256 2
# version 30001
Compared to old formate, the "_data" changes to "data_optics" and "data_particles" or "data_micrographs" and so on.
However, when I use relion_stack_create then import particle to cisTEM, it cannot work. It reported
Error: Encountered the following error - aborting :-
Error: Couldn't find _rlnDefocusU in star file (/ssd/relion_benchmark/to_cistem.star)
Now we have a script. Please email email@example.com to get the script.
cisTEM cannot read the new star file format yet. Just looking at what you wrote above - If you remove the data_optics section, then rename "data_particles" to _data it may work?
Can cisTEM be updated to handle both the RELION 3.0 star format AND the 3.1 format.
Or maybe a python script to convert the 3.1 format to 3.0 format, if possible?
we will work on supporting the new format in the next release. I'm sure conversion is possible, but I don't have a script for it now.
Thank you very much Tim for getting back to me.
I found in the paper "Estimation of High-Order Aberrations and Anisotopic Magnification from Cryo-EM Dataset in RELION-3.1 by Zivanov, Nakane, and Scheres; "SInce most of the optical properties of a particle are now defined through the optics group to which it belongs, each particle STAR file written out by RELION-3.1 now contains two tables: one listing the optics group and one listing the particles. The particles table is equivalent to the old one, except that certain optical properties are no longer listed"
I have just figure out to write a small program for convention these days. If you need it, should I email it to you?
I'd like to try some scripts to convert relion3.1 star file to other programs. Would you mind share your script with me?
Our company use email to sent it. Please email us (firstname.lastname@example.org) with your school+request script in title, and we will send it to you.
I am facing a problem with opening the previous project. The error message is as follows:
SQL Error: attempt to write a readonly database
Trying to execute the following command :-
int Database::ExecuteSQL(const char *)
+ Aborted cisTEM
Does anyone have a suggestion about what went wrong? I never have this issue before. I am using Centos 7.
It seems you don't have write access to the database, can you check the permissions?