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Perl Scripts for Use in NMR Structure Calculations

Written by: Melanie Nelson and Patty Fagan Jones, spring 1999

This document contains a list of Perl scripts that are helpful during calculations of NMR solution structures. This list may not be a complete list of all Perl scripts members of the lab use during structure calculations. Check Lena's Perl Scripts and Mike's Perl Scripts for more.

One method for running structure calculations involves using GENXPK, a program written by Garry Gippert. GENXPK can be used to assist in the initial assignment process, particularly if you are working on a mutant of a protein for which there are wildtype assignments. GENXPK can also be used to help assign NOEs. See the GENXPK manual (distributed with the software) or our wisdom page on using GENXPK to assign crosspeak for more information.

Scripts for converting between GENXPK and Felix97

• make_pat, which converts the GENXPK four column .assignments file to the format for Felix97 spin systems. This allows you to import assignments made previously in GENXPK into Felix, for use in a new Felix project.
  written by: Melanie Nelson
• pat_to_4col, which converts the Felix97 spin systems file to a GENXPK four column .assignments file. This allows you to export experiment specific frequency assignments from a Felix project to a .assignments file for use with GENXPK (for instance, to assign NOEs).
  written by: Melanie Nelson
• fix_4col. This script converts your Felix97 nomenclature to GENXPK nomenclature. This script is not yet tested with a stereopecific assignments file. You need to edit this script to make sure all of your residue and atom names are converted.
  SYNTAX: fix_4col basename.4col > .assignments
  written by: Patty Fagan Jones
• getref.mac, a Felix macro for extracting reference parameters for 3D matrices. Generates a refparm.noesy file, which is input for GENXPK.

Scripts for distance filtering

• disambig, which concatenates the ambiguity output from either GENXPK or Felix with the distance information for a family, from distance (part of Garry Gippert's GAP package). The atom names in the two files must match! Therefore, another version of this script is available, for cases where there is GENXPK format output with Felix-type atom nomenclature. This modified version also has the newer nomenclature for pseudoatoms. For instance, "QPA" is replaced by "QA", etc. All modifications are restricted to the ConvertGenxpkName subroutine. Users with Felix format ambiguity files may need to modify the ConvertFelixName subroutine. Another modified version of the script is required for GENXPK output from 3D data sets, due to the difference in column numbers in the ASG_RESULTS file. This script is called disambig3d, and was made using the modified version of disambig (disambig.mn). It is run exactly as disambig is.
  To use a disambig script:
  • Generate a list of unassigned NOEs, with the possible assignments, either using GENXPK or Felix. The comments in the script give examples of the correct format for these input files.
  • Generate a list of inter-atom distances for your current family of structures, using the distance program in Garry Gippert's GAP package. It is important that all the pseudoatoms are included in this distance file. Here is how I got that to work: 1) I used a modified pseudoatom map file, in which I had removed the pseudoatoms I did not want included. 2) I ran distance with the following command line:
    distance -fam family.fam -sub "^[HCMNQ]" -pms "^[HMNQ]" -pam pseudomap.mn -list 1 -cut 25 > output
    Refer to the help and documentation available for the distance program for more information about the command line options.
  • Run the script. The comments of the script give the command line:
    disambig -d [distance file] -f [felix|genxpk] -p [peak file]
  written by: Randal R. Ketchem; modified by Melanie Nelson
• aro_filt, which filters disambig output and only prints lines in which the potential assignment in D1 is an aromatic proton. It is for use with D₂O NOESY data. It is run as follows:
  aro_filt inputfile [>! output file]
  Where inputfile is the output from disambig.
  written by: Melanie Nelson
• doambig performs a similar function as disambig. The output can be sent to ambigrab to simplify the process of manually finding new assignments. Doambig screens through the unassigned peaks from one NOESY spectrum, based on the spectrum-specific assignments from that NOESY spectrum. doambig is a wrapper script which runs/requires the following scripts:
  • ambig2ncol (2D version) (3D version) (3D version with chemical shift filtering)
    Chemical shift filtering removes peaks from the file which arise within a user-defined chemical shift range, and is needed in the case where there are many unassigned resonances in this range, preventing unambiguous assignment of such peaks.
    Note: you need to edit the doambig script to correctly denote which of these three versions of ambig2ncol you wish to run. To test this script before running doambig, use the following syntax:
    ambig2ncol(.3d) -f [felix|genxpk] -p [peak file] -s [stereo file] > outputfile
  • noevio
  • all of the scripts and files in ~username/bin/ambi/ (check with anyone who has done structure calculations)
  • dofilter: This script can be commented out of the doambig script when doing manual distance filtering (early in your structure calculations). dofilter performs automated distance filtering. It uses ambipick and ambidis, which contain the filters that you will need to edit to do automated distance filtering.
  INPUT files:
  • noesyname_asgresults (called the "peak file", this is the GENXPK output file ASG_RESULTS renamed to noesyname_asgresults)
  • noesyname.ssa (stereospecific assignments file, can be empty)
  • family.all or family.fam (lists .pdb files)
  OUTPUT:
  • 7col.noesyname_asgresults
  • 7col.noesyname_asgresults.noevio (this file can be fed into ambigrab)
  • 7col.noesyname_asgresults.noevio.filter
  Edit doambig before running:
  • to point to the correct noesyname_asgresults file
  • to point to either family.all or family.fam file
  • to use the correct version of ambig2ncol (see the three versions above)
  Run doambig in your amber/rst/doambig/ directory.
  SYNTAX: doambig YYMMDD [monomer|dimer]
• ambigrab sorts the output from doambig and places asterisks next to the most probable assignments.
  INPUT files:
  • 7col.noesyname_asgresults.noevio
  OUTPUT:
  • filename designated in execute command
  Run ambigrab in your amber/rst/doambig/YYMMDD/ directory, where the doambig output is.
  SYNTAX: ambigrab -b ["bins"] -n [number of peaks] -p [peak file] > outputfile
  (for example, ambigrab -b "3 6 10" -n 8 -p 7col.cnoe_asgresults.noevio > 7col.cnoe_asgresults.noevio.8
  In this example, ambigrab places *** next to assignments with an avg. distance less than 3 angstroms, ** next to those which are 3 to 6 angstroms, and * next to those which are 6 to 10 angstroms.)
  
  • OPTIONAL: Before running ambigrab, you can run ambigroup. ambigroup outputs a list in which each line is
    [ambiguity, or # of assignment possibilities]: [number of peaks which display this ambiguity].
    SYNTAX: ambigroup 7col.noesyname_asgresults.noevio > outputfile
    

Additional scripts

• getratio, which reads a peaks file and a volume file (.xpk and .vol) generated from an HNHA spectrum, and calculates the ratio of the crosspeak (HN:HA) volume or intensity to the diagonal (HN:HN) volume or intensity. To use this script, you must first have picked and optimized the boxes for all of the peaks in the spectrum. I think it should be possible to get GENXPK to create the peakboxes, but I could not make it work. You must store intensities in the volume entity in Felix in order to use this script on intensities instead of volumes. There is a MSI supplied macro for this: relvolume.mac (in /usr/msi/970/felix/menus/mac). However, I could not get this to work on my 3D data set. All input files should be in Felix97 format.
  written by: Melanie Nelson
• maketable, a script which reads a file with chemical shift index information exported from Felix as text and the output file from getratio, and creates a plain text, tab-seperated file with the CSI and J-coupling data for each residue, useful for importing into a word processor or spreadsheet as a basis for tabulating information that defines the secondary structural elements in your structure. This script is a bit rough: it will only work for HA:HN coupling constants calculated with getratio and for one column of CSI data.
  written by: Melanie Nelson
• ambichemshift removes lines from an ambigrab group (or noevio) that contain any H betas or H gammas that are within the range (which you can modify) of 1.5 -2.5 ppm, in the case where there are many unassigned resonances in this range, preventing unambiguous NOE assignments. It is not clear how this script is run, so ambig2ncol was edited to insert the filter there.