The applications in Priism for aligning EM tomograms and computing the 3D reconstruction from the tomograms expect the tilt angles for the tomographic series to be stored in the extended header for the MRC data. If your data does not have the tilt angles in the extended header you can use the "Insert Tilts" application to add them. One way of checking the contents of a data set's extended header is to use the Edit Header application in Priism's DataViews->DataInfo menu.
The mass-normalization application also reads the exposure times for each projection in a projection series from the extended header. To handle that, "Insert Tilts" has the option to insert exposure times into the extended header as well.
To access the graphical interface, select "Processing", then "EM Processing", and, finally, "Insert Tilts" from the Priism menus. That will display a dialog. The first line in the dialog is for selecting your data which does not include the tilt angles. You can press the "Input" button to select the file with a file browser or directly enter the name of the file in the adjacent field. The second line in the dialog controls the name of the output MRC file. If your data does not already have space for the extended header, the tilt angles can not be inserted into it. Instead, the data will be copied to a new file which has space for the extended header; to select the name of the new file use the "Output" button to open a file browser or enter the name directly in the adjacent field. If your data has space for an extended header, you have the option of creating a new file with the updated tilt angles or modifying the existing file: turn on the "in place" button to modify the existing file or turn it off to create a new file.
The values for the inserted tilt angles are controlled by the third and fourth lines in the dialog. If the tilt angles are linearly spaced, you can turn on the "Linear spacing" button and enter the tilt angle, in degrees, for the first projection in the "Start" field and enter the tilt angle increment, in degrees, in the "Step" field. For other arrangements of the tilt angles, you will have to import the tilt angles from a text file by turning off the "Linear spacing" button and then pressing the "Tilt file" button to select a file or entering the name of the file directly in the adjacent field. The text file must have the tilt angles, in degrees, separated by whitespace and appear in the same order as the projections in the MRC file.
The values for the inserted exposure times are controlled by the fifth line in the dialog. The exposure times are always read from a text file. In the file, the exposure times must be separated by whitespace and appear in the same order as the projections in the MRC file. If you do not want to set the exposure times, do not enter a name for the file with the exposure times. If you only want to set the exposure times but not modify the tilt angles, turn off the linear spacing of the tilt angles, do not enter a name for the tilt angle file, and enter a name for the file with the exposure times.
Once you have selected the input file, tilt angles, exposure times, and, if necessary, the output file, press the "DoIt" button at the bottom of the dialog to insert the tilt angles and exposure times. You can use the "Close" button at the bottom of the dialog to dismiss the dialog.
The command to copy the contents of infile to outfile and insert linearly varying tilt angles which start with t degrees and have an increment of s degrees is
insert_tilts infile outfile -linear=t:s
To use the tilt angles read from the text file, tfile, instead of linearly varying tilt angles, you would use the following command:
insert_tilts infile outfile -tilt_file=tfile
To read the tilt angles from standard input, use the above command with a file name of "-" for the file with the tilt angles, i.e.:
insert_tilts infile outfile -tilt_file=-
If infile already had space for an extended header, the command to insert a linearly varying set of tilt angles is
insert_tilts infile -linear=t:s
and the command to insert the tilt angles read from a text file is
insert_tilts infile -tilt_file=tfile
To set the exposure times from values in a text file, efile, you could use
insert_tilts infile -exp_file=efile
or use any of the previous commands which also modify the tilt angles and
-exp_file=efile at the end of the command line.
To read the exposure times from standard input, use a single dash for
efile. Currently, insert_tilts can not read the tilt angles and
exposure times from standard input.
The example below copies the data from a.dat to a_h.dat and inserts tilt angles that start from 65 degrees and have an increment of -1 degrees. It also inserts the exposure times read from exposure.txt.
insert_tilts a.dat b.dat -linear=65:-1 -exp_file=exposure.txt
Priism | Edit Header | Bead alignment | Alignment and reconstruction | Iterative alignment and reconstruction | Mass-normalization |