email_test.py - testing
accessibility
of e-mail address for watch_magnet.py
watch_magnet3.py - Monitoring
the status of the Varian spectrometer (lock, temperature, overflows)
get_exp2.py - Utility to
download the experiment from the spectrometer
dof2_calc.py - dof2 calculation on Varian
watch_bruker.py - monitoring progress of acquisition on Bruker instrument (watches incrementation of time stamp on the fid files)
offset_calc.py - General utility for calculation of carrier offsets
water_shift.py - calculate water frequency for the specified temperature
calculate_time.py - analyses
the pulse sequence for delays and pulse lengths and
presents a summary which
enables you to calculate total
duration of the sequence
ek_rccpmg.py - generate lists of tau delays and number of cycles for rcCPMG experiment performed by ek_rccpmg15Ng pulse program. Usually resides with the spectral data from such an experiment.
analyze_interleaved_replicates.py - analyzes the spectral data from Bruker instrument acquired using pseudo 3D mode set up with ek_rccpmg.py to output serial numbers of planes for all specific CPMG frequencies
make_sp_files.py - Generates
the sparky .save files for a number of .sp files and the project using
common template file (without
MOLECULE/CONDITION set! - see next)
make_save_files.py - does
the same job but uses template file with MOLECULE/CONDITION set
unscrew_savefiles.py - make
.save and .proj files movable (replaces paths)
add_peak_labels.py - add consequtively numbered labels to ?-? peaks from automatic peak picking
import_xeasy.py - a utility to extract assignments from XEASY files and generate Sparky .save file. It also helps import assignment results from GARANT
predict_aa_type.py - an extension to run type_prob program by Grzesiek and Bax to predict amino acid type using carbon chemical shifts. Interactively select Ca and Cb peaks and get output of type_prob into a Python shell.
my_sparky_lib.py
er, zz - new_extension.py
eC - adjust_contours.py
ec - center_peaks.py
- ec
eO - center_one_peak.py
el - finding a list of peaks with intensities below specified S/N ratio (needs S/N specifically detemined by rm and inserted into st window , because automatic S/N measure is inaccurate)
check_low_intensity_peaks.py
copy_assignments_2.py
eo - detection of overlapped residues (assigned ones only) detect_overlap_sparky.py
detection tolerances are set in detect_overlap.ini
es - displaying a series of spectra as heights vs. index display_heights_vs_index.py
eS - (same as above) for VERY MANY spectra (such as large interleaved experiments) display_heights_vs_index.large_spectral_set.py
ef -
find_different_assignments.py
fold_assignments.py
ee - integrate.sp.py -
integration
of the peak (for subsequent fitting)
rm - regionrmsd.py
eh - relax_exponential_decay.py
- 'eh' enhanced version of 'rh'
relax_double_exponential_decay.
- didn't work
ea - update_assignments.py
xmgr.py
ed current_directory_to_sparky.py
- easier access to current directory:
eR - Recalculate relaxation times by equation - 'recalculate_times.py'
ex - xeasy.py - updated extension for output of XEASY format compatible with GARANT and PINE assignment programs.
Conversion of Sparky-exported spectral regions into small PNG files for HTML notebooks
eX - export_peak_snapshot.py - Exports a rectangular region around a selected peak for record-keeping, which is convertable to PNG for HTML documents using dat2png Matlab program.
NOTES on new Sparky extension development
add_peak_labels.py - add consequtively numbered labels to ?-? peaks from automatic peak picking
remove_residues.py -
Takes an lt-list 'source_list' of residues from Sparky and removes
from this list residues found in 'unwanted_list'. The result is
recorded in 'cleaned_up_list' and is importable into Sparky with 'ey'.
chem_shift_change.py -
calculation
of chemical shift changes in spectra
and generation of data arrays for titration curve analysis in MatLab
compare_protocols.py
- compare
differences between per-residue values
detect_overlap.py
- detect
overlap analyzing Sparky lists
remove_assignment_suffix.py - removes 'C-H' or like suffix from residue names in all the file
of a directory given as a
command line argument
Annn2nnn.py - strips 1st
letter from every line in the file so that the data
become importable to XMGR
LT_list_extract_column.py - extracts a column from Sparky LT list
es2xmgr.py - plotting of
'es' lists on XMGR as Height vs. Time
es2text.py - conversion of
'es' list into plain text 'x y dy' format with optional normalization
plot_data_Annn.py - plotting
a number of ANNN residue lists on XMGR (-diff, -reldiff)
plot_data_NNN.py - same for
just NNN format
plot_1vs2.py - plots one
dataset versus the other with errors
etaxyfit_xmgr_read.py
EtaxyR2ratio2.py
EtaxyR2ratio3.py
duplicate_errors.py - Error
analysis using duplicates in the time series
R1vsT_data_extract.py - in
multiple datasets: extract data for the same residue to XMGR vs.
parameter
sort_manual_list.py - Sorting
of manually prepared list of residues
smart_average.py - calculates
AVERAGE and SIGMA of full and x% trimmed dataset
trim_mean_sigma.py - (older
version - works only with Annn residue format)
trim_by_errors.py
- trimming of data by size of error column values
difference.py - calculate
difference between two datasets for residues found in both of them
dRex_calc.py
- calculation
of R2 difference between fast and slow pulsing datasets in rcCPMG
R1ro_R1_delta_calc.py - (ekn126)
pairwise analysis of R1rho-R1 data (small and large offset)
R1ro_deltaRex_calc.py - (ekn128)
Analysis of R1rho data combined with R1 data
rcCPMG R2 and simple Rex determination:
es2m.py - extract peak heights saved as 'es' list into format compatible with R2fitting/ (Matlab) . The program works in conjunction with ek_rccpmg.py and ek_rccpmg15N pulse program to produce data matrices for fitting relaxation dispersions.
rcCPMG Rex fitting :
es2m_full.py - extract peak heights saved as 'es' list into format compatible with RexFitting/ (Matlab) .
concatenate_intensity_data.py - This program concatenates datasets obtained in different rcCPMG experiments but at the same temperature. It allows fitting together data obtained at with different CPMG frequency tables.
make_prot_seq_files.py - The program to produce PROT and SEQ files required for GARANT and PINE assignment programs
equilibria.py
equilibria2.py
Ha_calc.py - calculation of activation energies from rate constants at different temperatures and prediction of constants at other temperatures
Pymol/ - collection of my old Pymol python programs
PymolLib.py - library of Pymol functions
pymol_start.pml - Run this in Pymol to set up paths for my PymolLib