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pipeline:subtract:centershift

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 pipeline:subtract:centershift [2021/02/01 16:08]shaikh pipeline:subtract:centershift [2021/10/11 17:15]shaikh Both sides previous revision Previous revision 2021/10/11 17:15 shaikh 2021/02/01 17:22 shaikh 2021/02/01 16:08 shaikh 2021/02/01 15:54 shaikh created Next revision Previous revision 2021/10/11 17:15 shaikh 2021/02/01 17:22 shaikh 2021/02/01 16:08 shaikh 2021/02/01 15:54 shaikh created Line 36: Line 36: The reconstruction will be roughly centered by alignment to a Gaussian blob of radius specified by the flag "--volradius". (Additional centering options will be provided in the future.) If the pixel size is provided (--apix), the units of radius will be assumed to be in Angstroms. If the pixel size is not provided, the radius will be assumed to be in units of voxels. If your structure is not globular, try the shortest dimension. The reconstruction will be roughly centered by alignment to a Gaussian blob of radius specified by the flag "--volradius". (Additional centering options will be provided in the future.) If the pixel size is provided (--apix), the units of radius will be assumed to be in Angstroms. If the pixel size is not provided, the radius will be assumed to be in units of voxels. If your structure is not globular, try the shortest dimension. - The output centered parameter file will be combine the Meridien parameters with the centering parameters.  The output reconstruction will not use smear information, and may be noisier than the reconstruction from the previous step. Simply make sure that the centering was adequate. The better the centering, the smaller the required shifts will be in subseuqnet refinements. + The output centered parameter file will be combine the Meridien parameters with the centering parameters.  The output reconstruction will not use smear information, and may be noisier than the reconstruction from the previous step. Simply make sure that the centering was adequate. The better the centering, the smaller the required shifts will be in subsequent refinements. \\ \\ ===== Input ===== ===== Input ===== === Main Parameters === === Main Parameters === - ; %%--%%cvol1 : First map to average and center. (default None) + ; %%--%%cvol1 : First map to average and center. (default required string) ; %%--%%cvol2 : Second map to average and center. (default None) ; %%--%%cvol2 : Second map to average and center. (default None) ; %%--%%shiftparams : Meridien parameters to combine with centering parameters. (default None) ; %%--%%shiftparams : Meridien parameters to combine with centering parameters. (default None) ; %%--%%diffimgs : Images from signal subtraction to reconstruct. (default None) ; %%--%%diffimgs : Images from signal subtraction to reconstruct. (default None) ; %%--%%outdir : Directory where outputs will be written. (default required string) ; %%--%%outdir : Directory where outputs will be written. (default required string) - ; %%--%%volradius : Radius to use for centering reconstruction. If the structure is not globular, try the shortest dimension. (default None) + ; %%--%%volradius : Radius to use for centering reconstruction. If the structure is not globular, try the shortest dimension. (default required string) ; %%--%%apix : Pixel size in Angstroms. (default None) ; %%--%%apix : Pixel size in Angstroms. (default None) Line 61: Line 61: ; params005_centered.txt : Parameters after centering ; params005_centered.txt : Parameters after centering + [{{:pipeline:subtract:dofinal.png?410 |Reconstruction (filtered) before centering}}][{{ :pipeline:subtract:centered.png?410|Reconstruction after centering}}] + \\ \\ ===== Description ===== ===== Description =====