e2refinetofrealign
This program ...
Options:
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--version |
bool |
show program's version number and exit |
-h |
--help |
bool |
show this help message and exit |
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--fbeaut |
bool |
(T/F)Apply extra real space symmetry averaging and masking to beautify final map prior to output |
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--fcref |
bool |
(T/F)Apply FOM filter to final reconstruction using function SQRT(2.0*FSC/(1.0+FSC)) |
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--ifsc |
string |
(0,1,2,3)Calculation of FSC Table (1,2,3 save reduce memory usage): 0 = Internally calculate two reconstructions with odd and even particles and generate FSC table at end. 1 = Only use odd particles for one reconstruction. 2 = Only use even particles for one reconstruction. 3 = use all particles but only for one reconstruction. |
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--fstat |
bool |
(T/F)Calculate additional statistics in resolution table at end (QFACT, SSNR, CC, etc.). T Uses more than 50% more memory. |
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--iblow |
string |
(1,2,4)Padding factor for reference structure. 4 uses the most memory but is the fastest search and refinement |
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--mask |
float |
Size of mask radius (RO). Default is 3/8 the particle radius * its angstrom per pixel |
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--rrec |
string |
Resolution of reconstruction in angstroms. It is the resolution to which the reconstruction is calculated. |
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--reslow |
float |
Resolution of the data included in the alignment. This is the low resolution value. ex:200 |
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--reshigh |
float |
Resolution of the data included in the alignment. This is the high resolution value. ex:25 |
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--refdef |
bool |
FreAlign will refine the defocus |
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--refastyg |
bool |
FreAlign will refine the astigmatism |
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--refpart |
bool |
FreAlign will refine the defocus for individual particles |
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--thresh |
float |
Phase Residual cutoff. Particles with a higher phase residual will not be included in the refinement |
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--pbc |
float |
Phase Residual/Pseudo B-Factor Constant |