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The project tree
The directory tree for a run is setup (see the page ARIA project preparation) by using:
aria2 -s project-xml
This command copies all different files required by ARIA (XML data files, CNS scripts, CNS parameter and topology files) into the same directory corresponding to the current run of the project (see ARIA project preparation for more details).
When running an ARIA project, all XML data-files as well as CNS files are read from the current run directory. In other words, only modifications of the files stored in the current run, are considered when re-running a project without setting it up first. The source-locations specified for the data in the project file are only used for project setup.
XML data-files are copied from their source locations (as specified in the project file) to the local "data" directory of the directory tree. All CNS-specific files (protocols, topology/parameters files etc) are copied from their source location (ARIA's installation path) into the local directory cns.
All data specified in the project XML file are copied to their respective subdirectories in run1/data. If user wants to make modifications to his data (after the project has been setup) he should edit the files run1/data/, the directory run1/cns/data is only used internally for structure calculation and should not be touched.
The directory tree for a typical ARIA run (run's nickname is "1") of nine iterations has the following structure:
| run1/data | local copies of the data files |
| run1/data/begin/ | storing the starting structure |
| run1/data/dihedrals/ | dihedral angle restraints |
| run1/data/distances/ | distance restraints |
| run1/data/hbonds/ | hydrogen bond restraints |
| run1/data/jcouplings/ | J-couplings restraints |
| run1/data/jrdcs/ | residual dipolar coupling restraints |
| run1/data/sequence/ | copy of the sequence XML file |
| run1/data/spectra/ | copies of the chemical shift and peak lists as XML files, reports about pre-assignment and filtering |
| run1/data/ssbonds/ | definition of the disulphide bonds |
| run1/data/templates/ | storing an initial ensemble |
| run1/data/hbonds/ | H-bond ".tbl" files |
| run1/structures/ |
structure calculation results, iteration reports, analysis results, cns output, etc. |
| run1/structures/it0/ | PDB, ".float", restraint files for the 0th iteration |
| run1/structures/it0/cns/ | the output files of CNS for the 0th iteration |
| run1/structures/it0/graphics/ | postscript files containing network-anchoring results |
| run1/structures/it1/ | PDB, ".float", restraint files for the 1th iteration |
| run1/structures/it1/cns/ | the output files of CNS for the 1th iteration |
| run1/structures/it1/graphics/ | postscript files containing the network-anchoring results and profiles for the violation RMS |
| .................................... |
................................... |
| run1/structures/it8/ | PDB, ".float", restraint files for the last iteration in this example, as well as the results of quality program analysis (PROCHECK, WHATIF, PROSA) |
| run1/structures/it8/cns/ | the output files of CNS for the last iteration |
| run1/structures/it8/graphics/ | postscript files containing the profiles for the violation RMS and the WHATIF quality profile along the residues. |
| run1/structures/it8/molmol/ |
files used to load the set of conformers and to visualize the restraint violations into MOLMOL |
| run1/structures/it8/analysis/ |
results of CNS analyses of the conformers |
| run1/structures/refine/ | directory for water/DMSO refined conformers, as well as the results of quality program analysis (PROCHECK, WHATIF, PROSA) |
| run1/structures/refine/graphics | postscript files containing the profiles for the quality profile along the residues. |
| run1/cns/ | storing CNS specific files |
| run1/cns/data/ | copies of data for CNS, created at the time of the run set-up. These data contain mainly restraints unambiguously defined during the set-up. |
| run1/cns/data/ssbonds/ |
definition of the disulphide bonds in CNS format |
| run1/cns/data/sequence/ | sequence in PDB format using CNS atom names created from the sequence XML file |
| run1/cns/data/rdcs/ | .tbl files for residual dipolar coupling restraints |
| run1/cns/data/hbonds/ | H-bond .tbl files |
| run1/cns/data/jcouplings/ | J-coupling ".tbl" files. Files belonging the same class are concatenated and stored in "c1.tbl", "c2.tbl", etc. |
| run1/cns/data/distances/ |
.tbl file for distance restraints |
| run1/cns/data/dihedrals/ | .tbl files for the dihedral angle restraints. |
| run1/cns/protocols/ | refinement protocols |
| run1/cns/protocols/analysis/ | analysis protocols |
| run1/cns/toppar/ | topology, linkage and parameter files |
| run1/cns/begin | PSF file, "_template" PDB file, swapping list, methyl list |
| run1/cache | cache file for faster re-runs |
ARIA is part of the ELIXIR infrastructure.