Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision | |||
|
auto3dem:history [2015/12/22 12:07] gcardone |
auto3dem:history [2015/12/22 12:59] (current) gcardone |
||
|---|---|---|---|
| Line 21: | Line 21: | ||
| == Random Model Computation == | == Random Model Computation == | ||
| - | * a minimum number of micrographs is used to generate an initial model. This value can be controlled by option //-nmgmin// in **setup_rmc** | + | * use inner radius given as input to **setup_rmc** to mask reference maps at each iteration |
| - | * initial master file contains commented line for limiting number of cpus used at reconstruction | + | * suppressed non significant warnings |
| - | + | ||
| - | == General modifications == | + | |
| - | * provided binary for CTFFIND4 in the package (Linux only) | + | |
| - | * at start programs will display if compiled in parallel or serial mode | + | |
| - | * maps are flattened with a soft mask, using full map as reference for masking in gold standard | + | |
| - | * inconsistency of pixel size in map header does not throw an error anymore | + | |
| == auto3dem == | == auto3dem == | ||
| - | * added parameter to control the soft edge with solvent flattening (//auto flatten_falloff//) | + | * added option //po2r mask_map// to specify a binary mask to use for mask-focused refinement |
| - | * keep input/output files used by flatten and hollow procedure | + | * added option //auto evod_parallel// to specify if processing of even- and odd-numbered particles to be done concurrently |
| - | * continue parameter file generated at end of each run has now unique name to avoid overwriting and to keep track of the processing | + | * added option //p3dr cpu_sparse// to specify if to spread cpus among different nodes to optimize resources for large maps (works only on multi-node clusters with pbs/sge queue systems) |
| + | * modified approach to define radial mask on maps (only ppft and hollow procedures): search of outer radius starts from radius with minimum standard deviation | ||
| == autopp == | == autopp == | ||
| - | * :!: option //D// modified to perform binning of micrographs instead of interpolation | + | * :!: restored option //D// to original interpolation and moved binning procedure to option //H// |
| - | * added experimental option 3x in autopp for using ctffind4 | + | * options 5 and 6: keep all info in first line of .dat files |
| + | * option 6: fixed bug when processing stacks with only one particle | ||
| + | * option j: when scaling, adjust also pixel size in .dat files | ||
| + | |||
| + | == PPFT == | ||
| + | * figure of merit calculated in double precision | ||
| + | |||
| + | == POR == | ||
| + | * avoid overflow error with metric/funcmode 0 | ||
| + | * change metric 1 to normalized version | ||
| + | * use the same user-defined metric for origin refinement | ||
| + | |||
| + | == maskmap == | ||
| + | * added option to apply the inverse of input mask | ||
| + | |||
| + | == rot_map == | ||
| + | * input shifts now expected as pixels | ||
| + | * improved estimate of the background value | ||
| + | * write the map in a format compatible with **p3dr** | ||
| - | == robem == | + | == a3dm_plot_fsc == |
| - | * added option for performing binning in batch mode (//-bin//) | + | * estimate resolution at threshold value by linear interpolation |
| - | * improved font appearance | + | * added option //-c/--cutoff// to specify threshold value where to estimate the resolution |
| - | * remove unused read/write menus | + | |
| - | * added warning if can not connect to display | + | |
| - | * minor fixes on size of file names | + | |
| - | * avoid including origin when calibrating maps for subtraction | + | |
| ==== auto3dem v4.05.1 ==== | ==== auto3dem v4.05.1 ==== | ||