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brungerlab
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pycresta
GNU General Public License v3.0
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Continuation options
#36
leitzj
opened
1 month ago
0
Sub-extraction is broken
#35
axelbrunger
opened
2 months ago
0
Extract: option to read both coordinates and angles
#34
axelbrunger
opened
9 months ago
0
Plot Back: generalize to class numbers greater than 9
#33
axelbrunger
closed
4 months ago
1
Plotback: the full tomogram has to have origin 0,0,0. Add an informative message to the Plotback info box.
#32
axelbrunger
closed
9 months ago
1
coordinate readers do not read floating point numbers
#31
axelbrunger
closed
4 months ago
2
Batch Extraction: overwriting of star files if there are duplicate tomogram names in different data collection directories
#30
axelbrunger
closed
9 months ago
1
Re-extraction does not work properly if two tomograms with identical names reside in different data collection directories
#29
axelbrunger
closed
4 months ago
1
Calculate angles will fail if some subtomograms are not created due to exceeding bounds of the tomogram
#28
axelbrunger
closed
9 months ago
1
Parallelize Re-extraction
#27
axelbrunger
closed
4 months ago
1
Visualize -> Accept/Reject fails if no star file is specified for filtered tomograms
#26
axelbrunger
closed
9 months ago
1
Revert to text boxes for specifying filenames and paths
#25
axelbrunger
closed
2 months ago
1
Re-Extraction: Please write .coords files in addition to .cmm files in the subcoord_files/ directories
#24
axelbrunger
closed
9 months ago
1
Please suppress messages in terminal window when plotting the Wiener filter function
#23
axelbrunger
closed
9 months ago
1
plot back works - useful for checking coordinate files
#22
axelbrunger
closed
1 year ago
1
Memory mapping for large mrc volumes (e.g., when using Filtering)
#21
axelbrunger
closed
4 months ago
0
Add the box size and pixel size as a comment into the cmm files written by Re-Extract
#20
axelbrunger
closed
4 months ago
1
Try Chimerax plugin ArtiaX, https://pubmed.ncbi.nlm.nih.gov/36251681/, https://onlinelibrary.wiley.com/doi/10.1002/pro.4472
#19
axelbrunger
closed
4 months ago
1
Explore implementation of tom_av3 alignment in pycresta
#18
axelbrunger
opened
1 year ago
0
Exception handling for extractions that straddle the border of the tomogram.
#17
axelbrunger
closed
9 months ago
2
Masking, Modify, and Plot Back: test that shifts from Star file are properly applied.
#16
axelbrunger
opened
1 year ago
0
Masking: index out of bounds error
#15
axelbrunger
opened
1 year ago
1
Perform tests to check consistency of box dimensions and pixel sizes
#14
axelbrunger
opened
1 year ago
0
Extraction: generalize parsing of coordinate files
#13
axelbrunger
closed
1 year ago
2
Modify: Set zero angles in new star file after star file or manual rotations.
#12
axelbrunger
closed
4 months ago
3
Modify: write info about star file and populate Master key at end of Modify -> Rotate... and -> Rotate Manually.
#11
axelbrunger
closed
4 months ago
2
Masking: populate Master Key at end of Masking
#10
axelbrunger
closed
4 months ago
1
Plot Back: - parallelization, test if works if star file refers to multiple tomograms, test multiple class feature
#9
axelbrunger
opened
1 year ago
1
Extraction: test calculation of angles in batch mode with multiple tomograms in one directory.
#8
axelbrunger
closed
9 months ago
1
Extraction: write info about star file, and populate Master Key at end of Extraction/Calculate Angles
#7
axelbrunger
closed
9 months ago
1
Extraction: Incorporate calc angles directly into Extraction as an option.
#6
axelbrunger
closed
9 months ago
1
Filtering (Gaussian option). Filtering: Each time pycresta creates a new directory with subtomograms, please write all information about settings and inputs as a text file into that directory, i.e., project text file.
#5
axelbrunger
closed
1 year ago
4
ATB added comments in various places in rot3d.c, pycresta.py, tom.py related to the various angle conventions and conversions.
#4
axelbrunger
closed
9 months ago
1
Plot back: mrc files sometimes were mapped to the same position in Chimera/ChimeraX
#3
axelbrunger
closed
1 year ago
1
Modify: ATManual (x,y,z) rottrans produces sometimes bus error when operating on previously rotated volumes
#2
axelbrunger
closed
1 year ago
1
Plot Back angles are wrong
#1
axelbrunger
closed
1 year ago
1