CARA Introduction

Introduction 

CARA stands for "Computer-Aided Resonance Assignment". It is written by Dr. Rochus Keller at the lab of of Prof. Kurt Wuthrich at ETH Zurich

CARA is a successor to XEASY. The main site for downloads and documentation is http://www.nmr.ch

Jump Start

1. Differences from XEASY
2. Starting a Structure Determination Project
   1. Loading a Repository Template
   2. Generating XEASY Sequence File
   3. Creating a New Project from XEASY Sequence File
   4. Loading NMR Spectra into Project
   5. Calibration and Folding
   6. Additional Parameters for GFT Spectra
3. Scopes - Displaying NMR Spectra

Templates

• BoR54_template.cara: GFT template from BoR54

LUA scripts

• Media:CARA_GFT_CABCA2CACB.lua: LUA script to calculate CA, CB, CA-1 and CB-1 shifts from GFT CA+/-CB and CA+/-CA shifts.

• Media:CARA_ExportToAutoAssign.lua: LUA script to generate AutoAssign input files. This script will create a table file and three sumulated peaklist files:
  • projectname.aat
  • hsqc.pks
  • hncacb.pks
  • hncocacb.pks

• Media:CARA_ImportFromAutoAssign.lua: LUA script to read sequential assignments from AutoAssign output. IMPORTANT! This script will overwrite existing assignments, if any!

• Media:CARA_GFT_CreateHABProjSpins.lua: LUA script to generate CA+/-HA and CB+/-HB shifts. IMPORTANT! This script will move existing GFT spins!

• Media:CARA_GFT_HABCAB2HAHBCACB.lua: LUA script to calculate HA and HB shifts from CA+/-HA and CB+/-HB. Missing CA and CB spins will be created, if possible. IMPORTANT! This script will move existing HA and HB spins!

• Media:CARA_CopyProjectedSpinsToOriginSystem2.lua: LUA script to copy projected spins. Modified version of the default CopyProjectedSpinsToOriginSystem script, allowing it to copy spins between systems, which are assigned to matching residues, but are not linked. N.B. - it is still recommended to have spin systems properly linked.

• Media:CARA_GFT_HCCH_calc.lua: LUA script to calculate aliphatic side-chain shifts

• Media:CARA_GFT_aroHCCH_calc.lua: LUA script to calculate aromatic side-chain shifts

• Media:CARA_ExportToCSI.lua: LUA script to prepare a CSI input file

-- AlexEletski - 06 Mar 2007

• Media:CARA_RemoveAllSpinLinks.lua: Removes all spinlinks

• Media:CARA_RemoveGFTSpins.lua: Removes all GFT-spins (spins, whose label contains a lowercase "p" or "m")

• Media:CARA_RemoveProjectedSpins.lua: Removes all spins with non-zero offset

• Media:CARA_CreateShortSequentialSpinLinks.lua: Simulates spin links from secondary structure. Takes the CSI output file and uses consensus secondary structure. Simulates HA(i) <-> HN(i+1), HB(i) <-> HN(i+1) for all residues. Simulates HN(i) <-> HN(i+1), HN(i) <-> HN(i+3) and HA(i) <-> HB(i+3) for residues in α-helices.

• Media:CARA_SparkyPeaklistToXeasy.lua: Converts Sparky-format peaklists to Xeasy-format peaklists. The resulting peaklists are not strictily compatible with XEASY - they are similar to the output of CYANA 2.1 and contain multiple assignments.

• Media:CARA_ImportCyana2xPeakList.lua: Reads peaklists in the format of CYANA 2.1 . Multiple assignments are read as "assignment guesses"

• Media:CARA_CreateConsensusPeakList.lua: Generates a "consensus" peaklist from two peaklists. Matching unique assignments are retained, mismatching assignments are converted to "assignment guesses".