Hi, great software!
I am trying manual refine with different masks, but in Results "job details" of any run always shows that automasking is Yes, while Supplied Mask is Yes when it is actually not supplied, and shows No when it was actually supplied, and Mask ID is 0, although it was not 0 as entered in GUI.
Is that a bug? Is there any way to see actual full log file of the job? Correct mask seems to be used during the run, but it will be nice to be able to see it later as well.
Thanks,
Leonid
Hi Leonid,
Yes there is a bug in reading the information back out of the database in the current version - it should be fixed in the next release.
There is no output file from the jobs, everything is just stored in the database, however it is possible to retrieve the information yourself directly from the database using the following scheme :-
1. First you must open your database in sqlite, so run :-
sqlite3 name_of_project.db2. Run an sql query, e.g :-
select * from refinement_details_***;You must replace *** with the refinement_id number.
Instead of doing
select *you can just give a comma separated list of the columns you want, e.g :-select SHOULD_USE_SUPPLIED_MASK, OUTSIDE_MASK_WEIGHT, MASK_FILTER_RESOLUTION from refinement_details_***;I have listed all the columns in refinement_details below, you can select from them or If you select *, then the columns returned are in the order below.
Cheers,
Tim
-------------------------------
List of columns :-
-------------------------------
CLASS_NUMBER
REFERENCE_VOLUME_ASSET_ID
LOW_RESOLUTION_LIMIT
HIGH_RESOLUTION_LIMIT
MASK_RADIUS
SIGNED_CC_RESOLUTION_LIMIT
GLOBAL_RESOLUTION_LIMIT
GLOBAL_MASK_RADIUS
NUMBER_RESULTS_TO_REFINE
ANGULAR_SEARCH_STEP
SEARCH_RANGE_X
SEARCH_RANGE_Y
CLASSIFICATION_RESOLUTION_LIMIT
SHOULD_FOCUS_CLASSIFY
SPHERE_X_COORD
SPHERE_Y_COORD
SPHERE_Z_COORD
SPHERE_RADIUS
SHOULD_REFINE_CTF
DEFOCUS_SEARCH_RANGE
DEFOCUS_SEARCH_STEP
AVERAGE_OCCUPANCY
ESTIMATED_RESOLUTION
RECONSTRUCTED_VOLUME_ASSET_ID
RECONSTRUCTION_ID
SHOULD_AUTOMASK
SHOULD_REFINE_INPUT_PARAMS
SHOULD_USE_SUPPLIED_MASK
MASK_ASSET_ID
MASK_EDGE_WIDTH
OUTSIDE_MASK_WEIGHT
SHOULD_LOWPASS_OUTSIDE_MASK
MASK_FILTER_RESOLUTION
Great, thanks a lot, that helps!