CARA Introduction: Difference between revisions

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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  


=== Jump Start  ===
*[[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]]
 
 
GFT template example


#[[CARA vs Xeasy|Differences from XEASY]]  
*[[Media:BoR54_template.cara|BoR54_template.cara]]: GFT template from BoR54
#Starting a Structure Determination Project
##[[CARA New Template|Loading a Repository Template]]
##[[CARA One Letter File To Seq File|Generating XEASY Sequence File]]
##[[CARA Create Project From Seq|Creating a New Project from XEASY Sequence File]]
##[[CARA Load Spectra|Loading NMR Spectra into Project]]
##[[CARA Calibration And Folding|Calibration and Folding]]
##[[GFT Spectra Parameters|Additional Parameters for GFT Spectra]]
#[[CARA Scopes|Scopes - Displaying NMR Spectra]]


=== Templates  ===


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


=== LUA scripts ===
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.
*[[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.


*[[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_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>projectname.aat</tt>  
**<tt>hsqc.pks</tt>  
**<tt>hsqc.pks</tt>  
Line 31: Line 25:
**<tt>hncocacb.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_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 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%/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


<br>-- AlexEletski - 06 Mar 2007
*[[Media:CARA_ExportToCSI.lua|ExportToCSI.lua]]: LUA script to prepare a CSI input file


<br>
*[[Media:CARA_RemoveAllSpinLinks.lua|RemoveAllSpinLinks.lua]]: Removes all spinlinks


*[[NESG:%ATTACHURL%/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%/RemoveGFTSpins.lua|RemoveGFTSpins.lua]]: Removes all GFT-spins (spins, whose label contains a lowercase "p" or "m")
*[[Media:CARA_RemoveProjectedSpins.lua|RemoveProjectedSpins.lua]]: Removes all spins with non-zero offset


*[[NESG:%ATTACHURL%/RemoveProjectedSpins.lua|RemoveProjectedSpins.lua]]: Removes all spins with non-zero offset
*[[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%/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.
*[[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%/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_ImportCyana2xPeakList.lua|ImportCyana2xPeakList.lua]]: Reads peaklists in the format of CYANA 2.1 . Multiple assignments are read as "assignment guesses"


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

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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