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== CARA ==
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 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


CARA is a successor to XEASY. The main site for downloads and documentation is http://www.nmr.ch
*[[CARA vs Xeasy|Differences from XEASY]]
*[[Calibration And Folding in CARA|Calibration and Folding]]
*[[GFT Spectra Parameters in CARA|Additional Parameters for GFT Spectra]]
*[[CARA Scopes|Scopes - Displaying NMR Spectra]]


=== Jump Start ===


# [[NESG:CARAvsXeasy|Differences from XEASY]]
GFT template example
# Starting a Structure Determination Project
## [[NESG:CARANewTemplate|Loading a Repository Template]]
## [[NESG:OneLetterFileToSeqFile|Generating XEASY Sequence File]]
## [[NESG:CARACreateProjectFromSeq|Creating a New Project from XEASY Sequence File]]
## [[NESG:CARAloadSpectra|Loading NMR Spectra into Project]]
## [[NESG:CalibrationAndFolding|Calibration and Folding]]
## [[NESG:GFTSpectraParameters|Additional Parameters for GFT Spectra]]
# [[NESG:CARAScopeS|Scopes - Displaying NMR Spectra]]


=== Templates ===
*[[Media:BoR54_template.cara|BoR54_template.cara]]: GFT template from BoR54


* [[NESG:%ATTACHURL%/BoR54_template.cara|BoR54_template.cara]]: GFT template from BoR54


=== LUA scripts ===


* [[NESG:%ATTACHURL%/GFT_CABCA2CACB.lua|GFT_CABCA2CACB.lua]]: LUA script to calculate CA, CB, CA-1 and CB-1 shifts from GFT CA+/-CB and CA+/-CA shifts.
LUA scripts


* [[NESG:%ATTACHURL%/ExportToAutoAssign.lua|ExportToAutoAssign.lua]]: LUA script to generate AutoAssign input files. This script will create a table file and three sumulated peaklist files:
*[[Media:CARA_GFT_CABCA2CACB.lua|GFT_CABCA2CACB.lua]]: LUA script to calculate CA, CB, CA-1 and CB-1 shifts from GFT CA+/-CB and CA+/-CA shifts.
** <tt>projectname.aat</tt>
** <tt>hsqc.pks</tt>
** <tt>hncacb.pks</tt>
** <tt>hncocacb.pks</tt>


* [[NESG:%ATTACHURL%/ImportFromAutoAssign.lua|ImportFromAutoAssign.lua]]: LUA script to read sequential assignments from AutoAssign output. '''IMPORTANT!''' This script will overwrite existing assignments, if any!
*[[Media:CARA_ExportToAutoAssign.lua|ExportToAutoAssign.lua]]: LUA script to generate AutoAssign input files. This script will create a table file and three sumulated peaklist files:
**<tt>projectname.aat</tt>
**<tt>hsqc.pks</tt>
**<tt>hncacb.pks</tt>
**<tt>hncocacb.pks</tt>


* [[NESG:%ATTACHURL%/GFT_CreateHABProjSpins.lua|GFT_CreateHABProjSpins.lua]]: LUA script to generate CA+/-HA and CB+/-HB shifts. '''IMPORTANT!''' This script will move existing GFT spins!
*[[Media:CARA_ImportFromAutoAssign.lua|ImportFromAutoAssign.lua]]: LUA script to read sequential assignments from AutoAssign output. '''IMPORTANT!''' This script will overwrite existing assignments, if any!


* [[NESG:%ATTACHURL%/GFT_HABCAB2HAHBCACB.lua|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_GFT_CreateHABProjSpins.lua|GFT_CreateHABProjSpins.lua]]: LUA script to generate CA+/-HA and CB+/-HB shifts. '''IMPORTANT!''' This script will move existing GFT spins!


* [[NESG:%ATTACHURL%/CopyProjectedSpinsToOriginSystem2.lua|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_HABCAB2HAHBCACB.lua|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!


* [[NESG:%ATTACHURL%/GFT_HCCH_calc.lua|GFT_HCCH_calc.lua]]: LUA script to calculate aliphatic side-chain shifts
*[[Media:CARA_CopyProjectedSpinsToOriginSystem2.lua|CopyProjectedSpinsToOriginSystem2]]: 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.


* [[NESG:%ATTACHURL%/GFT_aroHCCH_calc.lua|GFT_aroHCCH_calc.lua]]: LUA script to calculate aromatic side-chain shifts
*[[Media:CARA_GFT_HCCH_calc.lua|GFT_HCCH_calc.lua]]: LUA script to calculate aliphatic side-chain shifts


* [[NESG:%ATTACHURL%/ExportToCSI.lua|ExportToCSI.lua]]: LUA script to prepare a CSI input file
*[[Media:CARA_GFT_aroHCCH_calc.lua|GFT_aroHCCH_calc.lua]]: LUA script to calculate aromatic side-chain shifts


*[[Media:CARA_ExportToCSI.lua|ExportToCSI.lua]]: LUA script to prepare a CSI input file


-- AlexEletski - 06 Mar 2007
*[[Media:CARA_RemoveAllSpinLinks.lua|RemoveAllSpinLinks.lua]]: Removes all spinlinks


*[[Media:CARA_RemoveGFTSpins.lua|RemoveGFTSpins.lua]]: Removes all GFT-spins (spins, whose label contains a lowercase "p" or "m")


* [[NESG:%ATTACHURL%/RemoveAllSpinLinks.lua|RemoveAllSpinLinks.lua]]: Removes all spinlinks
*[[Media:CARA_RemoveProjectedSpins.lua|RemoveProjectedSpins.lua]]: Removes all spins with non-zero offset


* [[NESG:%ATTACHURL%/RemoveGFTSpins.lua|RemoveGFTSpins.lua]]: Removes all GFT-spins (spins, whose label contains a lowercase "p" or "m")
*[[Media:CARA_CreateShortSequentialSpinLinks.lua|CreateShortSequentialSpinLinks.lua]]: Simulates spin links from secondary structure. Takes the CSI output file and uses consensus secondary structure. Simulates HA(i) &lt;-&gt; HN(i+1), HB(i) &lt;-&gt; HN(i+1) for all residues. Simulates HN(i) &lt;-&gt; HN(i+1), HN(i) &lt;-&gt; HN(i+3) and HA(i) &lt;-&gt; HB(i+3) for residues in α-helices.


* [[NESG:%ATTACHURL%/RemoveProjectedSpins.lua|RemoveProjectedSpins.lua]]: Removes all spins with non-zero offset
*[[Media:CARA_SparkyPeaklistToXeasy.lua|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.


* [[NESG:%ATTACHURL%/CreateShortSequentialSpinLinks.lua|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 &alpha;-helices.
*[[Media:CARA_ImportCyana2xPeakList.lua|ImportCyana2xPeakList.lua]]: Reads peaklists in the format of CYANA 2.1 . Multiple assignments are read as "assignment guesses"


* [[NESG:%ATTACHURL%/SparkyPeaklistToXeasy.lua|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_CreateConsensusPeakList.lua|CreateConsensusPeakList.lua]]: Generates a "consensus" peaklist from two peaklists. Matching unique assignments are retained, mismatching assignments are converted to "assignment guesses".


* [[NESG:%ATTACHURL%/ImportCyana2xPeakList.lua|ImportCyana2xPeakList.lua]]: Reads peaklists in the format of CYANA 2.1 . Multiple assignments are read as "assignment guesses"
[[Category:CARA]][[Category:Resonance_Assignment]]
 
* [[NESG:%ATTACHURL%/CreateConsensusPeakList.lua|CreateConsensusPeakList.lua]]: Generates a "consensus" peaklist from two peaklists. Matching unique assignments are retained, mismatching assignments are converted to "assignment guesses".

Latest revision as of 19:27, 9 December 2009

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


GFT template example


LUA scripts

  • GFT_CABCA2CACB.lua: LUA script to calculate CA, CB, CA-1 and CB-1 shifts from GFT CA+/-CB and CA+/-CA shifts.
  • 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
  • ImportFromAutoAssign.lua: LUA script to read sequential assignments from AutoAssign output. IMPORTANT! This script will overwrite existing assignments, if any!
  • GFT_CreateHABProjSpins.lua: LUA script to generate CA+/-HA and CB+/-HB shifts. IMPORTANT! This script will move existing GFT spins!
  • 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!
  • CopyProjectedSpinsToOriginSystem2: 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.
  • RemoveGFTSpins.lua: Removes all GFT-spins (spins, whose label contains a lowercase "p" or "m")
  • 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.
  • 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.
  • ImportCyana2xPeakList.lua: Reads peaklists in the format of CYANA 2.1 . Multiple assignments are read as "assignment guesses"
  • CreateConsensusPeakList.lua: Generates a "consensus" peaklist from two peaklists. Matching unique assignments are retained, mismatching assignments are converted to "assignment guesses".
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