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NMR Scripts for Analysis and Display

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The following scripts and little programs were written by Dr. Debbie Shalev.

Please reference them "written by Deborah E. Shalev, The Wolfson Centre of Applied Structural Biology, The Hebrew University of Jerusalem, Israel".

They are used in conjunction with AURELIA, XPLOR, MARDIGRAS, MolMol, PROCHECK and/or InsightII.
The programs they are used with must also be referenced accordingly.
 

Scripts A to I
Scripts L to Z
XPLOR to MARDIGRAS Translation

Queries and comments are welcome.

Last updated November, 2003


 Scripts A to I      Scripts L to Z       XPLOR to MARDIGRAS translation
Script Name
Usage
Synopsis 
accept2refine
accept2refine filename
Text editor that changed the word "accept" to "refine" in all occurrences. 
all_stats
all_stats file_series max_file_number
To be used on the results of a pro_run (from PROCHECK) run. Creates filename_stats and filename_gen_stats including the secondary structure and Ramachandran analysis of the files. Also creates rama_cp that creates a sequential series of pdbs that fulfill Ramachandran criteria. Must be performed from within the directory where accept.pdbs are. 
analysis
analysis
To be used in conjunction with "viol". Reads output from viol, low_energy.file, and creates MolMol.mac files: analysis.mac - A general file that reads the molecules into MolMol. superimpose.mac - This file superimposes according to the desired range. color_by_energy.mac - changes colors according to energy. These can be read in as macros int MolMol.
analysis_MSI
analysis_MSI
To be used in conjunction with "viol". Reads output from viol, low_energy.file, and creates  .log files: analysis.log - A general file that reads the molecules into InsightII. superimpose.log - This file superimposes according to the desired range. color_by_energy.log - changes colors according to energy. These can be sourced by INSIGHT (Accelyrs).
anglepar
anglepar
Script to make a file that shows the missing angle parameters from xplor while making non- canonical elements for xplor. Creates file angle.par that must be edited. 
bondpar
bondpar
Script to make a file that shows the missing bond parameters from xplor while making non- canonical elements for xplor. Creates file bond.par that must be edited.
check_ppms
check_ppms filename
Input is aurelia-format noe file. Output is a file containing peak assignments that are not identical. 
cleanup_prorun
cleanup_prorun (in correct directory)
Use in directory where prorun was run. Removes all prorun results WITH NO WARNING.
clear_pdbs
clear_pdbs (in correct directory)
This program removes all pdb and pdb_* files resulting from an XPLOR run, and the display files. IT GIVES NO WARNING. 
count_i
count_i filename
Input is xplor-format noe file. Counts the number of noes of different ranges. Warns if there is inconsistency between original file and results. 
erase_color
erase_color
Uses results of analysis. Creates .log files for MSI that erase structures in a given color.
erase_x
erase_x filename
Erases any line containing the character x. 
f2h
f2h file.par
Use with xplo2D to change all fluorine atoms and values to those of hydrogen. 
get_violations.inp
get_violations.inp
Copies the file violation.inp to working directory. Edit every {====>} according to needs.
h2f
h2f filename
Use with xplo2D to change all hydrogen atoms and values to those of fluorine. 
improppar 
improppar
Make a file showing xplor missing parameters. Used while making non-canonical elements for xplor. Put file in appropriate place in your .par file and edit.

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 Scripts A to I      Scripts L to Z       XPLOR to MARDIGRAS translation
 
 
list_peaks
list_peaks filename
Uses aurelia format peak volume output to provide a list of peaks that appear in the file. 
local_RMSD
local_RMSD
Interactive program that creates a series of xplor average.pdb files with local RMSD's and creates a file with the values.
markout
markout filename_noe.tbl
Erases lines in xplor-format noe table that are not xplor-readable ("!", "x", "?", "u", "l", etc.)
noe_stats
noe_stats noe_filename
Counts the number of noes from every residue to those preceding it and reports. 
noe_viol
noe_viol(only if violations.file is available)
Part of viol program: takes violations.file (output from viol) and lists the number of noe violations of each kind in order of the most violations to the least. 
noesy_ranges
noesy_ranges filename
Takes an xplor-format noe.tbl file and changes the noes to ranges.
pro_run
pro_run pdb-prefixes resolution-angstrom max-file-number storage-directory
This program runs the program procheck on a series of pdb files. You must source mycom and ccp44 to run it (Contact Debbie for this)
rm_run
rm_run
Will remove all xplor results in the current directory. WITH NO WARNING.
rmsd_stats
rmsd_stats
Must be used from within xplor directory where noe_viol.file resides.This program reads noe_viol.file and prints out the deviations ofBonds, Angles, Impropers, NOE, and CDIH
separate_noe_file
separate_noe_file filename
This program takes and xplor-format noe file and separates it into 5 new files that are i, i+1, i+2, i+3 and i-lr (long-range) noes.
seq_noe_count
seq_noe_count noe_filename
Is supposed to count the number of noes from every residue to that preceeding it and report.
sort_assignment
sort_assignment filename
Interactive prog-let to produce supplementary file from noe.tbl file, ready for publication.
sort_peaks
sort_peaks filename
This program puts the xplor-format noe file into numerical order.
super_new
super_new
Interactive program that creates a new file superimpose_ .log that can be used to superimpose all the files over a chosen file. 
viol
viol Xplor must be sourced and violations.inp must be appropriately edited. This program creates a number of useful files: violations.file - all violations; energy.file - energies of structures; low_energy.file - ascending energies of structures; noe_viol.file noe violations only; noe_viol_count.file - number of times specific noe violation occurs. Also created a file called energy_cp that, when run, will create a set of files names by ascending energies.
wuth_plot
wuth_plot filename Creates a postscript file with a Wuthrich plot for the input peptide from an xplor-format noe file. YOU HAVE TO EDIT THE LENGTH OF THE PEPTIDE.

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 Scripts A to I      Scripts L to Z       XPLOR to MARDIGRAS translation
 
 
 
The following files should be used together, sequentially for XPLOR to MARDIGRAS/CORMA translation
find_used_peaks
find_used_peaks .noe.tbl .aurelia
Search for the common peaks based on noe.tbl file input. Find them in aurelia file. Output .aurelia.used. Needs XPLOR type file and aurelia format peak volume list
make_xplor2mardi
make_xplor2mardi filename.used
Must be used in conjunction with aurelia format peak volume list. Creates filename.used.xplor2mardi which must be edited manually to change XPLOR format to MARDIGRAS/CORMA format.
make_mardi_INT_file
make_mardi_INT_file .xplor2mardi_file .aurelia_file.used newfilename
This program creates a MARDIGRAS INT file (for Corma and Mardigras) from an aurelia output file. NOTE - no "."s in the INT filename or CORMA won't read it. The intensities are normalized to the largest one. 
make_cormain_input
make_cormain_input root_of_pdb_list
Creates file cormain.input which contains corma.in commands for cut and paste. Output from corma.in is a list of cin*.pdb in corma.in format. 
make_corma_input
make_corma_input root_of_pdb_list
Creates file corma.input which contains corma.in commands for cut and paste. Output from corma will be C* sets of files for each cin*.pdb file. 

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