ARIA - start a new project

Start a new ARIA project with SPARKY data:

1. Edit the directory names:

For 2D spectra:
Your SPARKY NOE list file contains lines like this:

      Assignment         w1         w2        Volume    Fit Height 



         L21HA-HB2      1.435      1.877   4.86e+08 ga       319789 

               ?-?      3.776      3.218   3.12e+08 ga       205476 

               ?-?      2.257      2.833

For 3D spectra:
Your SPARKY NOE list file contains lines like this:



      Assignment         w1         w2         w3        Volume   Data Height 



             ?-?-?      3.977     45.152      3.982   9.89e+10 lo    186256688 

     I41HD#-CD-HD#      0.818     12.622      0.820   4.10e+10 lo    116163264 

   Y26HD#-E28CA-HA      7.338     56.052      4.257   6.76e+09 lo       670847 

    W76HE3-CE3-HE3      7.491    120.787      7.492                  -26023680 

             ?-?-?      7.474     38.300      1.776                      88271

For 4D spectra:
Your SPARKY NOE list file contains lines like this:

 

      Assignment         w1         w2         w3         w4        Volume   Data Height 



   M36HN-N-Y26N-HN      9.519    122.013    119.995      8.770   2.09e+08 ga       598397 

           ?-?-?-?      6.958    120.361    120.502      8.659   2.06e+08 ga       200166

The chemical shift list:
Your SPARKY ppm list file contains lines like this:

 

 Group   Atom  Nuc    Shift   SDev  Assignments 

  

     R2     CA  13C   56.539  0.003      3 

     R2     CB  13C   30.808  0.009      3 

     R2     CD  13C   43.363  0.000      1 

     R2     CG  13C   27.114  0.005      2 

     R2     CO  13C  176.552  0.000      1 

     R2     HA   1H    4.373  0.007      2 

     R2    HB#   1H    1.828  0.000      2 

     R2    HD#   1H    3.172  0.000      1 

     R2    HG#   1H    1.647  0.002      2 

     G3     CA  13C   45.191  0.022      5 

     G3     CO  13C  174.024  0.000      1 

     G3    HA#   1H    3.985  0.003      3 

     G3     HN   1H    8.659  0.002     17 

     G3      N  15N  111.115  0.009     17 

     S4     CA  13C   58.312  0.000      1 

     S4     CB  13C   63.882  0.000      1 

     S4     HN   1H    8.251  0.002      9 

     S4      N  15N  115.445  0.027      9 

     H9     CA  13C   55.976  0.016      2

Please take a look at your NOE list files first before filling out the following form. You have to specify in which of the 2, 3 or 4 ppm columns (counted from left to right and from 1 to 4) the heteronuclei and protons can be found (If you make a mistake here, all the assignments will be messed up!).
In the 2D case both heteronuclei have to be set to not available. In the 3D case the heteronucleus 2 has to be set to not available.
The PPMD values are the deltas for the chemical shifts which build the frequency windows for the assignment of the NOE peaks. They have to be specified for every used frequency of all the spectra.
You need to specify a sequence as a sequence file or as a PDB file. A sequence file should only contain amino acids in 3-letter code (with spaces or linebreaks as dividers) like that:
ASP GLU GLY TRP
The segid must have 4 characters or must be blank.
You have to specify absolute paths for all files and directories.
Don't use pathnames with more than 80 characters (otherwise CNS will complain).
Unused fields blank.
Always be careful and take a look at the generated .tbl files in the corresponding spectrum directory.

Current ARIA program directory:           
Path of the new project:                  
Run number:	                          

SPECTRUM 1: Name:                         
            NOE list file:	          
            ppm list file:	          
            NOE volume or intensity:      
            Heteronucleus 1:              
            Proton 1:                     
            Heteronucleus 2:              
            Proton 2:                     
            PPMD for Heteronucleus 1:     
            PPMD for Proton 1:            
            PPMD for Heteronucleus 2:     
            PPMD for Proton 2:            
            Use which peaks:              

SPECTRUM 2: Name:                         
            NOE list file:		  
            ppm list file:                
            NOE volume or intensity:      
            Heteronucleus 1:              
            Proton 1:                     
            Heteronucleus 2:              
            Proton 2:                     
            PPMD for Heteronucleus 1:     
            PPMD for Proton 1:            
            PPMD for Heteronucleus 2:     
            PPMD for Proton 2:            
            Use which peaks:              

SPECTRUM 3: Name:                         
            NOE list file:                
            ppm list file:                
            NOE volume or intensity:      
            Heteronucleus 1:              
            Proton 1:                     
            Heteronucleus 2:              
            Proton 2:                     
            PPMD for Heteronucleus 1:     
            PPMD for Proton 1:            
            PPMD for Heteronucleus 2:     
            PPMD for Proton 2:            
            Use which peaks:              

SPECTRUM 4: Name:                         
            NOE list fe:                  
            ppm list file:                
            NOE volume or intensity:      
            Heteronucleus 1:              
            Proton 1:                     
            Heteronucleus 2:              
            Proton 2:                     
            PPMD for Heteronucleus 1:     
            PPMD for Proton 1:            
            PPMD for Heteronucleus 2:     
            PPMD for Proton 2:            
            Use which peaks:              

SPECTRUM 5: Name:                         
            NOE list file:                
            ppm list file:                
            NOE volume or intensity:      
            Heteronucleus 1:              
            Proton 1:                     
            Heteronucleus 2:              
            Proton 2:                     
            PPMD for Heteronucleus 1:     
            PPMD for Proton 1:            
            PPMD for Heteronucleus 2:     
            PPMD for Proton 2:            
            Use which peaks:              

Sequence or PDB file:           
Unambiguous distance restraints:
Ambiguous distance restraints:  
Dihedral angle restraints:      
Karplus restraints 1:           
Karplus restraints 2:           
Karplus restraints 3:           
Karplus restraints 4:           
Karplus restraints 5:           
Residual dipolar couplings 1:   
Residual dipolar couplings 2:   
Residual dipolar couplings 3:   
Residual dipolar couplings 4:   
Residual dipolar couplings 5:   
Hbonds restraints:              
CSI file:                       
CSI dihedral restraints errors: 
TALOS pred file:                
TALOS error factor:             
TALOS minimum error:            
Segid of the protein:

Start a new ARIA project with SPARKY data:

1. Edit the directory names:

2. Please save the updated parameters somewhere in a directory as new.html:

3. Type ARIA on the UNIX command line in that directory where you have saved your new.html.