single data block example
In this example, we will use starfile to read and write a STAR file with a single data block.
particles.star
data_particles
loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnAngleRot #4
_rlnAngleTilt #5
_rlnAnglePsi #6
_rlnMicrographName #7
91.798700 83.622600 203.341030 -51.740000 173.930000 32.971000 01_10.00Apx.mrc
97.635800 80.437000 203.136160 141.500000 171.760000 -134.680000 01_10.00Apx.mrc
92.415200 88.842700 210.663900 -78.750000 173.930000 87.263200 01_10.00Apx.mrc
94.607830 93.135410 205.425960 -85.215000 167.170000 85.632200 01_10.00Apx.mrc
86.187800 80.125400 204.558750 14.910000 163.260000 -16.030000 01_10.00Apx.mrc
91.824240 76.738300 203.794280 39.740000 168.410000 -57.250000 01_10.00Apx.mrc
98.253300 73.530100 203.856030 73.950000 166.380000 -84.640000 01_10.00Apx.mrc
101.303500 80.290800 194.790400 -178.878000 166.090000 73.181000 01_10.00Apx.mrc
Read the file
import starfile
df = starfile.read('particles.star')
Interact with the data
df['rlnCoordinateX'] += 10
df.head()
rlnCoordinateX rlnCoordinateY rlnCoordinateZ rlnAngleRot rlnAngleTilt rlnAnglePsi rlnMicrographName
0 101.79870 83.62260 203.34103 -51.740 173.93 32.9710 01_10.00Apx.mrc
1 107.63580 80.43700 203.13616 141.500 171.76 -134.6800 01_10.00Apx.mrc
2 102.41520 88.84270 210.66390 -78.750 173.93 87.2632 01_10.00Apx.mrc
3 104.60783 93.13541 205.42596 -85.215 167.17 85.6322 01_10.00Apx.mrc
4 96.18780 80.12540 204.55875 14.910 163.26 -16.0300 01_10.00Apx.mrc
Note
Simple data blocks (unlike those using the loop_ notation) will return a python dictionary instead of a dataframe:
Save the (modified) data to file
starfile.write(df, 'modified_particles.star')
For files containing multiple data blocks, please see the multiple data block example.