Embedded Files
PISEMA Automated Conversion Script
PISEMA Automated Conversion Script
PISEMAautoconvert.com is a c-shell script that automatically reads a Bruker acquired PISEMA data set, extracts all the necessary parameters and processes the data using NMRPipe. The program nmrDraw is called up automatically to read in the processed data for phasing in the 15N dimension by the user. The processed data in NMRPipe format is then converted to SPARKY .ucsf format and the user can convert the Bruker processed PISEMA dataset to SPARKY as well for comparison.
Requirements for running PISEMAautoconvert.com
- Computer with a UNIX operating environment
- NMRPipe installed and in system path
- Sparky installed and in system path (specifiically need pipe2ucsf)
- Experiment directory for a Bruker acquired PISEMA data set, directory should contain ser, acqu, acqus, acqu2, acqu2s files and pdata directory
HSQC Automated Conversion Script
HSQC Automated Conversion Script
HSQCautoconvert.com is a c-shell script that automatically reads in Varian formatted data acquired utilizing the gNhsqc BioPack pulse sequence. The script extracts all the necessary parameters and processes the data using NMRPipe. The program nmrDraw is called up automatically for 1H and 15N phasing by the user. Processed and phased data can then be converted to SPARKY .ucsf format if desired. HSQCautoconvert.com requires a computer with a UNIX operating environment, NMRPipe installed and in system path, Sparky installed and in system path (specifically need pipe2ucsf), and an experiment directory containing the data file (fid) and parameter file (procpar). HSQCautoconvert.com utilizes the GM lineshape filter to improve linewidths and forward-backward linear prediction to improve resolution in the 15N dimension.
Requirements for running HSQCautoconvert.com
- Computer with a UNIX operating environment
- NMRPipe installed and in system path
- Sparky installed and in system path (specifiically need pipe2ucsf)
- Experiment directory for a Varian acquired gNhsqc data set, directory should contain fid and procpar files.
PDB Formatted Structure Family Statistics Script
PDB Formatted Structure Family Statistics Script
PDBStructStats.com is a c-shell script that automatically reads in a family of structures (for example those generated by XPLOR-NIH) and sorts the family according to total energy. The script outputs a list (EnergyStats.txt) listing the entire structure family in order from lowest to highest energy. The number of each structure is displayed along with the energy and total number of violations.
Requirements for running HSQCautoconvert.com
- Computer with a UNIX operating environment
- A directory containing only PDB files for the structure family. All pdb files should have the same name followed by a four digit sequential number (i.e. structure0000.pdb, structure_0001.pdb, ...., structure_0199.pdb, structure_0200.pdb).
MatLab Script: PISA Wheel Simulation
MatLab Script: PISA Wheel Simulation
This MatLab script will calculate a PISA wheel for a single helix tilt angle. Values for Phi, Psi, and tau can be changed as desired. Values for the chemical shift tensor and bond angles are consistent with previous literature and simulations and change to these values should be avoided.
MatLab Script: Randomized Phi, Psi PISA Wheel Simulation
MatLab Script: Randomized Phi, Psi PISA Wheel Simulation
This MatLab script uses the randomized points from the script above to plot PISA wheels with randomized variations in phi and psi torsion angles.
MatLab Script: Randomized Phi, Psi PISEMA Data Calculation
MatLab Script: Randomized Phi, Psi PISEMA Data Calculation
This MatLab script will calculate the PISEMA data points for x number of resonances with randomized variation in phi and psi torsion angles as defined in ‘aphv’. This script saves the data points as a .mat file which is read into the script in D.3 for plotting. Note, this script must be run once for each desired torsion angle range (i.e. ± 8°, ± 16°). The filename defined in ‘fid’ must also be changed for each repetition and must match the values found in script below.
"Grant us to know that it is not the beginning, but the continuing of the same until it is thoroughly finished, that yieldeth the true glory."~ Sir Francis Drake
Report abuse