Auto3DEM ver. 4.04

[Giovanni Cardone]

We are pleased to announce the immediate availability of a new release of AUTO3DEM.
In addition to minor bug fixes, there are few changes that are noteworthy:- the license ha been changed to follow the recommendations of the University. Essentially the software is free to use, modify and distribute for research purposes;
- better support of large maps (>1200 pixels along each size);
- the program auto3dem now enforces a resolution-limited approach when automatically determining the resolution range to use for determining the particle parameters, in order to minimize noise overfitting;
- auto3dem: added option for automatically determining, at each iteration, the optimum radial range to use for masking the reference map (auto hollow_auto). To use in combination with 'auto hollow_map' set to 1;
- auto3dem: provide by default an optimum radial range for template masking at the end of the Random Model Computation;
- added new program, flatten, to  automatically remove background density from the reference map, and added an option in auto3dem (auto flatten_map) to set to 1 in order to use it.
- the metrics for determining the alignment in PO2R have been optimized and now they all report their values as phase residuals, in degrees (soon an exact formulation for all of them will be provided);
- the first line of the parameter (i.e. dat) files can now include, after the name of the stack, 3 fields describing the box size of the particles (along x and y) and the number of particles. These values are optional but most of the programs add them, in order to minimize the access to the stack file;
- auto3dem: changed behavior of ‘auto freeze_res’ in order to only freeze the range of resolution frequencies used for determining particle parameters, but to allow the reconstruction to be performed according to the resolution estimated;
- the routine for CTF refinement has been improved and the way it is controlled by auto3dem has changed. Another email will follow shortly with some information about it.
You can look at the modification history (file MINOR_RELEASE_NOTES) for a list of all the changes.

Sincerely,
Giovanni

PS: this is a second attempt to send this email. If already received, please disregard.