film vs. filament number in a frealign .par file for helical refinement

Submitted by dlyumkis on Thu, 2012-10-25 17:01

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Frealign

Hi,
I have a question regarding the use of the "FILM" parameter in a helical refinement. During a normal single-particle refinement, the parameter "FILM" in a .par file should correspond to the electron micrograph from which the particle was selected (e.g. for defocus, magnification refinement, etc.). However, when I refine a helix and utilize the "set_polarity.exe" program to adjust the angles, I notice that it's reading the "FILM" column and labeling it as a single filament. My question then is, in a helical refinement, does the "FILM" label correspond to the micrograph or the specific helical filament (of which there can be more than 1 in a single micrograph)?

niko Thu, 2012-10-25 17:48

Yes, the FILM number in a particle parameter file corresponds to one filament when using Frealign with helical symmetry. It allows set_polarity to check that all segments within one filament are pointing in the same direction.