Faculty of Science |
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.
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Scripts
A to I Scripts L to
Z XPLOR
to MARDIGRAS translation
Script Name
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Usage
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Synopsis
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accept2refine
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accept2refine filename
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Text
editor that changed the word "accept" to "refine" in all occurrences.
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all_stats
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all_stats file_series max_file_number
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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.
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analysis
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analysis
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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
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analysis_MSI
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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).
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anglepar
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anglepar
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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.
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bondpar
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bondpar
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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.
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check_ppms
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check_ppms
filename
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Input
is aurelia-format noe file. Output is a file containing peak assignments
that are not identical.
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cleanup_prorun
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cleanup_prorun
(in correct directory)
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Use
in directory where prorun was run. Removes all prorun results WITH NO WARNING.
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clear_pdbs
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clear_pdbs (in correct directory)
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This
program removes all pdb and pdb_* files resulting from an XPLOR
run, and the display files. IT GIVES NO WARNING.
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count_i
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count_i filename
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Input
is xplor-format noe file. Counts the number of noes of different ranges.
Warns if there is inconsistency between original file and results.
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erase_color
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erase_color
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Uses
results of analysis. Creates .log files for MSI that erase structures in a given color.
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erase_x
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erase_x filename
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Erases
any line containing the character “x”.
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f2h
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f2h file.par
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Use
with xplo2D to change all fluorine atoms and values to those of hydrogen.
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get_violations.inp
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get_violations.inp
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Copies
the file violation.inp to working directory. Edit every {====>} according to needs.
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h2f
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h2f filename
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Use
with xplo2D to change all hydrogen atoms and values to those of fluorine.
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improppar
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improppar
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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
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list_peaks
filename
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Uses
aurelia format peak volume output to provide a list of peaks that appear in the file.
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local_RMSD
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local_RMSD
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Interactive
program that creates a series of xplor average.pdb files with local RMSD's
and creates a file with the values.
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markout
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markout filename_noe.tbl
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Erases
lines in xplor-format noe table that are not xplor-readable ("!", "x", "?", "u", "l", etc.)
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noe_stats
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noe_stats noe_filename
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Counts
the number of noes from every residue to those preceding it and reports.
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noe_viol
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noe_viol(only if violations.file is available)
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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.
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noesy_ranges
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noesy_ranges filename
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Takes
an xplor-format noe.tbl file and changes the noes to ranges.
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pro_run
pdb-prefixes resolution-angstrom max-file-number storage-directory
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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)
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rm_run
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rm_run
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Will
remove all xplor results in the current directory. WITH NO WARNING.
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rmsd_stats
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rmsd_stats
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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
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separate_noe_file
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separate_noe_file filename
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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.
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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 | 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. |
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
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find_used_peaks
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find_used_peaks .noe.tbl .aurelia
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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
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make_xplor2mardi
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make_xplor2mardi filename.used
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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.
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make_mardi_INT_file
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make_mardi_INT_file
.xplor2mardi_file .aurelia_file.used newfilename
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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.
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make_cormain_input
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make_cormain_input root_of_pdb_list
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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.
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make_corma_input
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make_corma_input root_of_pdb_list
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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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Copyright ©, 1997, The Hebrew University of Jerusalem. All Rights Reserved |