Questions about particle locations

[ariel234156]

Hello,
When I upload the coordinates of particles (spk file), is there an option to upload also the angles between the [x,y,z]? This means instead of three parameters, the file will contain six, and the NextPYP will know to align each particle depending on the angles between the different planes [xy,xz,yz].
Thank you.

[abartesaghi]

nextPYP retrieves particle orientation information from the frealign/*_volumes.txt file, not from the *.spk files. This file is generated after you import the coordinates and contains all the particles in your dataset.

If you need to provide external angles, you'll have to edit this file yourself.

The format is as follows:

number  lwedge  uwedge  posX    posY    posZ    geomX   geomY   geomZ   normalX normalY normalZ matrix[0]       matrix[1]       matrix[2]        matrix[3]       matrix[4]       matrix[5]       matrix[6]       matrix[7]       matrix[8]       matrix[9]       matrix[10]       matrix[11]      matrix[12]      matrix[13]      matrix[14]      matrix[15]      magnification[0]       magnification[1]      magnification[2]        cutOffset       filename
1       -60.00  60.08   64      64      64      128     128     128     -17.143361      -17.1434        21.518059       1       0       0       0       0       1       0       0       0       0       1       0       0       1       1       1       1       0       /path_to_project/sva/tilt10_spk0000.rec

After the first header line, each subsequent line should correspond to a single particle, and you can use the columns normalX, normalY, and normalZ to specify the external angles. The last column in this file contains the name of the sub-volume file, which in this case is /path_to_project/sva/tilt10_spk0000.rec.

Once you have this file, make sure to select it for the Alignments from sub-volume averaging (*.txt) option in the Refinement tab of the Particle refinement block downstream.