Frealix: getting started & example: calculating an FSC
Usage
Frealix doesn't have a GUI, and is normally invoked with one command-line argument:
frealix parameters.flx
where parameters.flx is a flat-text file (the extension is not important) with a key,value pair on each line, separated by spaces or tabs.
One special parameter which must always be specified is FREALIX_MODE, which specifies the mode, or command you want Frealix to execute.
Example: computing an FSC with Frealix
For example, if you want to compute the FSC between two volumes, you would use FREALIX_MODE CALC_FSC. Your parameter file (called fsc.flx, say) would then look something like this:
FREALIX_MODE CALC_FSC
INPUT_VOLUME_1 vol_1.mrc # The first 3D reconstruction
INPUT_VOLUME_2 vol_2.mrc # The second 3D reconstruction
Note that Frealix can read and write MRC, Spider and Imagic files and that comments (with # or !) are ignored as well as lines with unrecognized parameter keys.
You would then run Frealix like this:
frealix fsc.flx
The output from Frealix will look something like this:
** Welcome to Frealix **
Version: 0.0.0
SVN revision: 1201
Build date: Jan 02 2013
Debug symbols?: No
Control filename: tmp.flx
User name (home directory): alr99 (/gusr/alr99/linux)
Working directory: /scratch/alr99/frealix_nightly_test/test_suite/tmv_synth_refine_
Command line: /scratch/alr99/frealix_nightly_130102/build_intel/frealix tmp.flx
Host name: hamburg.rose2.brandeis.edu
Host, machine type: x86_64-linux, x86_64
OpenMP threading available?: No
Date & time: 2013-01-03 01:03:31
Frealix will run its CALC_FSC mode
Frealix is running in its CALC_FSC mode
Mode description: Add description here
Run-time parameters:
Key Value Set by user? Description
INPUT_VOLUME_1 2OM3_200_h_200_m.mrc T Input volume 1
INPUT_VOLUME_2 3drec_straight_hm.mrc T Input volume 2
Shell FSC
0 1.000
1 0.998
2 0.995
3 0.985
4 0.974
5 0.985
6 0.975
7 0.965
8 0.988
9 0.992
10 0.997
11 0.992
12 0.983
13 0.950
14 0.960
15 0.959
16 0.973
17 0.960
18 0.956
19 0.959
20 0.956
21 0.975
22 0.981
23 0.983
24 0.982
25 0.983
26 0.989
27 0.988
28 0.981
29 0.985
30 0.983
31 0.987
32 0.981
33 0.974
34 0.972
35 0.963
36 0.970
37 0.973
38 0.973
39 0.978
40 0.983
41 0.979
42 0.979
43 0.970
44 0.979
45 0.979
46 0.978
47 0.973
48 0.978
49 0.977
50 0.974
51 0.967
52 0.963
53 0.962
54 0.965
55 0.953
56 0.939
57 0.943
58 0.930
59 0.900
60 0.917
61 0.920
62 0.897
63 0.872
64 0.864
65 0.854
66 0.841
67 0.843
68 0.824
69 0.818
70 0.798
71 0.754
72 0.752
73 0.734
74 0.690
75 0.705
76 0.714
77 0.700
78 0.696
79 0.674
80 0.676
81 0.616
82 0.604
83 0.610
84 0.605
85 0.581
86 0.576
87 0.577
88 0.576
89 0.550
90 0.546
91 0.537
92 0.529
93 0.536
94 0.524
95 0.550
96 0.525
97 0.518
98 0.534
99 0.561
100 0.554
2013-01-03 01:03:32: FREALIX says goodbye (total execution time: 1 second)
There are a few things to note here:
- No matter what mode Frealix is running, the last line will say "goodbye" when it terminated normally and "sorry" when there was an error.
- The first part of the output is common to all modes, it lists useful information such as Frealix's version number (0.0.0 indicates that a non-released, development version is used), system information etc.
- This is followed by a summary of all input run-time parameters (in our case, just two:
INPUT_VOLUME_1andINPUT_VOLUME_2), their values, whether they were set by the user (F indicates that hard-coded default values were used because the parameter was not found in the parameter file given) and a short description of the parameter's meaning or effect.
