|
|
| (13 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| == 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]]
| |