Refine

Merging Refinement

Refine Defocus? [refdefocus]

Switch, deciding if defocus should be refined.

Refine tilt geometry (only in 3D mode)? [reftiltgeo]

Define if during the refinement step also the tilt geometry should be refined. This is done by the MRC program origtilt, which compares the current dataset from one tilted image with the 3D dataset, to find a better tilt geometry. Use with caution, and only on well advanced dataset.

Refine Beamtilt (only in 3D mode)? [refbeamtilt]

Switch, deciding if beamtilt should be refined. This needs a fairly advanced dataset. Expected beam tilt values should be in the order of a few milirads, not larger.

Refine Merging Settings

Refine setting for revhk switch? [refrevhk]

Switch, deciding if the settings for revhk should be verified. revhk decides if data for H and K should be exchanged. See also rotrev.

Refine setting for rot90 switch? [refrot90]

Switch, deciding if the settings for rot90 should be verified. rot90 decides if data should be rotated by 90 deg about z. See also rotrev.

Refine setting for rot180 switch? [refrot180]

Switch, deciding if the settings rot180 should be verified. rot180 decides if data should be rotated by 180 deg about z. See also rotrev.

Refine setting for sgnxch switch? [refsgnxch]

Switch, deciding if the settings sgnxch should be verified. sgnxch decides if data should be flipped around the A axis. That means K=-K, Z=-Z. See also rotrev.

Refine setting for revhnd switch ? (ATTENTION, this changes handedness!)

Switch, deciding if the settings for the handedness should be verified. revhnd decides if handednes should be inverted. That means Z=-Z.

Refine setting for revxsgn switch ? (ATTENTION, this changes handedness!) [refrevxsgn]

Switch, deciding if the settings revxsgn should be verified. revxsgn decides if the H index for the data should be inverted. That means H=-H. See also rotrev.

Refine sign of tilt angle (invert_titlangle)? (ATTENTION, this changes handedness!) [refinvert_tiltangle]

Switch, deciding if the sign of the tilt angle should be verified.

Parameter Refinement

Refine [Refine]

Choose what to refine. 1. Defocus 2. Defocus and Astigmatism 3. Tilt Axis 4. Tilt Angle 5. All together

Refine Lattice? [Refine_Lattice]

Defines if the lattice should be refined.

Number of Cycles [refine_cyc]

Choose the number of iterative cycles of refinement.

Reference dataset for refinement [refine_reference]

Choose the merged dataset that should be used for refinement.

Overwrite data in database? [refine_overwrite]

Switch, deciding if the determined (refined) values should overwrite the current values in the image database.

maska refinement values (start, end, step, factor) [refine_maska_val]

List for refinement of the Fourier filter radius for the first unbending, in RLU (reciprocal lattice units).

boxa1 refinement values (start, end, step) [refine_boxa1_val]

List for refinement of the diameter of the reference for the first unbending, in pixel.

maskb01 refinement values (start, end, step, factor) [refine_maskb01_val]

List for refinement of the Fourier filter radius for the first round of the second unbending, in RLU (reciprocal lattice units).

maskb02 refinement values (start, end, step, factor) [refine_maskb02_val]

List for refinement of the Fourier filter radius for the second round of the second unbending, in RLU (reciprocal lattice units).

boxb1 refinement values (start, end, step) [refine_boxb1_val]

List for refinement of the diameter of the reference for the second unbending, in pixel.

Refine maska? [refine_maska_doit_1] [refine_maska_doit_2] [refine_maska_doit_3]

Flag, defining if maska should be refined, using the corresponding values from values refine_maska_val.

Refine boxa1? [refine_boxa1_doit_1] [refine_boxa1_doit_2] [refine_boxa1_doit_3]

Flag, defining if boxa should be refined, using the corresponding values from values refine_boxa1_val.

Refine maska and boxa1 simultaneously [refine_maska_boxa1_doit]

Flag, defining if maska and boxa1 should be refined, using the corresponding values.

Refine maskb01? [refine_maskb01_doit_1] [refine_maskb01_doit_2] [refine_maskb01_doit_3]

Flag, defining if maskb01 should be refined, using the corresponding values from values refine_maskb01_val.

Refine boxb1? [refine_boxb1_doit_1] [refine_boxb1_doit_2] [refine_boxb1_doit_3]

Flag, defining if boxb1 should be refined, using the corresponding values from values refine_boxb1_val.

Refine maskb01 and boxb1 simultaneously [refine_maskb01_boxb1_doit]

Flag, defining if maskb01 and boxb1 should be refined, using the corresponding values.