Resonance Assignment/CARA: Difference between revisions

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== Loading a new template  ==
The topics below provide an overview of resonance assignment of 15N,13C-labeled proteins using CARA. For more information and tutorials please consult [http://www.nmr.ch CARA web site].


To start a new structure determination project in CARA you need to load a template. A template is a CARA repository without project that contains definitions for residue types, spectrum type and LUA scripts. You can either load the default template from the [http://www.cara.ethz.ch/Wiki/TemplatesPage templates page] of the official CARA web-site, or extract a template from an existing CARA repository.
*[[CARA Introduction|Introduction]]
*[[CARA vs Xeasy|Differences from XEASY]] 
*[[CARA Scopes|Scopes - Displaying NMR Spectra]]


In CARA click '''File -> New from template''' and select the appropriate <tt>.cara</tt> file. For detailed instructions see [http://www.cara.ethz.ch/Wiki/ImportingTemplate]


<br>[[Image:CARA New Template Dialogue.png]]  
*[[Resonance Assignment/CARA/Starting a new project|Starting a new project]]
*[[Resonance Assignment/CARA/Backbone assignment|Backbone resonance assignment]]
*Side Chain Assignment
**[[Aliphatic Side Chain Assignment with CARA|Aliphatic side-chain assignment]]
**[[Aromatic Side Chain Assignment with CARA|Aromatic side-chain assignment]]
**[[Amide Side Chain Assignment with CARA|Amide side-chain assignment]]
*[[SSAFromFractional13CLabeledSample|Stereospecific Assignment of Leu and Val Isopropyl Groups]]
*[[Creating NOESY peaklists with CARA|Creating NOESY peaklists]]


CARA Template for GFT spectra [[Media:BoR54_template.cara|BoR54_template.cara]]: Latest GFT template for BoR54 project


== Starting a new project ==
Also see [[Resonance_Assignment/CARA/Backbone_assignment_GFT|backbone assignment with GFT spectra]]
 
Normally you would create a new project based on a protein sequence in XEASY format.
 
If you have the protein sequence in one-letter format you can convert it to XEASY <tt>.seq</tt> file the following way:
#Save the one-letter sequence in a <tt>.aa</tt> file, e.g. <tt>foo.aa</tt>
#Execute '''OneLetterFileToSeqFile''' LUA script from '''Terminal''' tab of the main window. Select your <tt>.aa</tt> file as input and give full path for the output <tt>.seq</tt> file.
 
[[Image:CARA One Letter to Seqfile.png]]
 
To create a new project for you protein in the repository right-lick '''Projects''' -> '''Import Project from Sequence...'''. Select the corresponding <tt>.seq</tt> file in the file explorer and click on the '''Residues''' button in the pop-up menu.
 
[[Image:CARA proj import from seq.png]]
 
This will create a project entry with the same name as the *.seq file, with the sequence field appropriately filled and all other fields empty. The new project will have the same name as the provided <tt>.seq</tt> file, though it can be renamed.
 
[[Image:CARA new project.png]]
 
Even though a repository can contain several projects, it is a good practice to have only one project per repository. For example, many LUA scripts assume that there is a single project in a repository.
 
You can also import a project from a BMRB file. In this case chemical shift data will be imported in addition to the sequence. For more details see [http://www.cara.ethz.ch/Wiki/CreateNewProject]. Also check the page on importing XEASY files: [http://www.cara.ethz.ch/Wiki/WorkingWithOtherProgramsImportExport]
 
 
 
 
 
#[[CARA Introduction|Introduction]]
#[[Spin System Identification with CARA|Spin System Identification in 2D 15N-HSQC and 3D HNNCO]]
#[[Backbone Assignment with CARA|Backbone Resonance Assignment]]
#[[HA and HB Assignment with CARA|Assignment of HA and HB Resonances with (4,3)D GFT HABCAB(CO)NHN]]
#Side Chain Assignment
##[[Aliphatic Side Chain Assignment with CARA|Aliphatic side-chain assignment]]
##[[Aromatic Side Chain Assignment with CARA|Aromatic side-chain assignment]]
##[[Amide Side Chain Assignment with CARA|Amide side-chain assignment]]

Latest revision as of 20:13, 8 August 2012

The topics below provide an overview of resonance assignment of 15N,13C-labeled proteins using CARA. For more information and tutorials please consult CARA web site.



Also see backbone assignment with GFT spectra

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