Project

Presentation

The xml file describing the project contains all the information needed to run an ARIA calculation. The input data are included in the file as links to other files, whereas the parameters of the calculation are written into the file. The project file is the main file used to start a run.

List of attributes

The following attributes are contained into the Project xml file:

• element project:

<project name="" version="1.0" author="" date="" description="" comment="" references="" 
working_directory="/home/Bis/terez/ARIA/test" temp_root="/home/Bis/terez/ARIA/test" 
run="1" file_root="my_molecule" cache="yes" cleanup="yes">

• working_directory: Defines the root directory of your project. Every run is then stored in a separate sub-directory [working_directory]/runxxx.
• temp_root: For every run, ARIA creates a directory [temp_root]/aria_temp.@xxxxx to store all temporary (large) files (e.g. CNS output). If omited, the current directory will be used. When calculating on multiple machines, the temporary directory *must* be accessible from all machines.
• run: Specifies the current run of a project. Every RUN is stored in a separate directory with the project directory as its root, i.e. [working_directory]/runxxxx.
• file_root: The file_root is used to build filenames. E.g., if the file_root is set to "my_structure", the structure PDB-files are called my_structure_1.pdb etc.
• cache: If enabled, ARIA caches all XML data-files (i.e. molecule definition and spectra). If a RUN is executed more than once, ARIA just accesses the cache instead of reading the complete XML files; this considerably speeds-up the reading process. If the original data (i.e. those that are stored in the run's local data-directory [working_directory]/RUNxxx/data) are modified, the cache is automatically invalidated so that the data are read from their original XML files.
• cleanup: Enable this option if you want ARIA to remove the temporary directory [temp_root]/aria_temp.@xxxxx. Of course, the main temporary directory, [temp-root], is not removed.

• section data:

  <data>
   <ccpn_model filename=""/>
   <molecule file="/home/Bis/bardiaux/projects/tudor/xml/tudor.xml" 
       format="xml" ccpn_id="">
     <linkage_definition name="automatic" filename=""/>
     <parameter_definition name="automatic" filename=""/>
     <topology_definition name="automatic" filename=""/>
   </molecule>
   <spectrum enabled="yes" use_assignments="no" trust_assigned_peaks="no" 
       structural_rules="no" filter_diagonal_peaks="no"	filter_unassigned_peaks="no">	
     <shifts file="/home/Bis/bardiaux/projects/tudor/xml/13C.ppm.xml" 
       format="xml" ccpn_id="" default_shift_error="0.0"/>
     <peaks file="/home/Bis/bardiaux/projects/tudor/xml/13C.noesy.xml" 
          format="xml" ccpn_id="" peak_size="volume" 
          freq_window_proton1="0.04" freq_window_hetero1="0.5" 
          freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
     </peaks>
     <experiment_data molecule_correlation_time="0.0" 
        spectrum_mixing_time="0.0" 
        spectrometer_frequency="0.0" ambiguity_type="intra"/>
   </spectrum>	
   <dihedrals file="" format"tbl" ccpn_id="" enabled="yes" data_type="talos"/>
   <symmetry enabled="no" method="standard" n_monomers="1" symmetry_type="None" ncs_enabled="no" packing_enabled="yes"/>
   <initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
  </data>

• In the element ccpn_model, if the data are read from a CCPN project, the CCPN project filename is given in the attribute 'filename' and the other attributes 'file' should be empty. In that case, during the loading step, ccp_id attributes are automatically generated corresponding to the molecules and to the spectra picked up by the user in the CCPN project. If the data are read from xml files, all attributes 'ccpn_id' should be empty.
  
• the elements linkage_definition, parameter_definition and topology_definition define the linkage, parameter and topology files used in CNS. These parameters can 'automatic', and the files to use are then determined from the molecular system. If the parameters are 'user-defined', the corresponding filename should be given as an attribute. The attributes 'lower_bound_correction' and 'upper_bound_correction' describe the lower and upper bound values used for violated restraints, if the bound-correction is enabled. When performing a Violation Analysis on an ensemble of structures, ARIAs default approach is to deactivate a restraint for the structure calculation in the subsequent iteration, if the restraint has been violated in more than a certain fraction of all structures. 

• In spectrum, if the element use_assignment is set to “no”, any existing peak assignment is discarded and peaks are re-assigned automatically. This option overrides the attribute “trust_assigned_peaks”.
• If the element trust_assigned_peaks is set to “yes”, fully assigned peaks are always used for structure calculation and can never be removed from the restraint list – even if the violation-analysis classifies it as violated. If set to “no”, fully assigned peaks are treated in the normal way, i.e. they can be removed from the restraint list if violated but their assignments are never changed. It is also possible to control that behavior for every single cross-peak separately. Every cross-peak has an attribute, “reliable” (cf. Spectrum-xml). If set to “yes”, the respective peak never gets rejected by the violation-analysis.
• Structural_rules are only valid for symmetric multimers assignments. If the two implicated atoms belong to the same secondary structure element and if they are separated by more than 5 residues (helix) or 4 residues (beta strands), the assignment possibility could be inter-molecular only. Secondary structure definition is taken from the “structure” attribute of each residue. This filter is not used if the peak is set as reliable.
• If the element filter_diagonal_peaks is enabled, diagonal peaks will be removed.
• If the element filter_unassigned_peaks is set to yes, unassigned peaks will be removed.

• If lower_bound-correction is turned on (attribute enabled in the element lower_bound_correction), ARIA runs a 2-pass Violation Analysis: the 1st pass determines the set of violated restraints which is then analysed further: if the restraint is still violated with respect to the user-defined LOWER bound (attribute value in the element lower_bound_correction), nothing changes. If not, the restraint will be used (with modified lower bound) in the subsequent iteration.
• If upper_bound-correction is turned on (attribute enabled in the element upper_bound_correction), ARIA runs a 2-pass Violation Analysis: the 1st pass determines the set of violated restraints which is then analysed further: if the restraint is still violated with respect to the user-defined UPPER bound (attribute value in the element upper_bound_correction), nothing changes. If not, the restraint will be used (with modified upper bound) in the subsequent iteration.
  
• The peak volumes or intensities can be taken as input using the peak_size attribute of the element peak. The frequence window defining the ambiguity of the chemical are defined in ppm. The attribute default_shift_error gives the default error [ppm] of chemical-shift measurementsfor which an error is not available.
  
• The element experiment contains parameters useful if the spin diffusion correction of the distance bounds is activated. 

• The element ambiguity_type allows to specify the level of ambiguity: intra: NOEs involving atoms from one monomer only, inter: NOEs involving atoms from different monomers, all: no known information, all NOEs are ambigous in terms of monomer.
• In dihedral the element format specifies the format in which your data is represented. This can either be TALOS format (“tbl”) or a CCPN data model (“ccpn”)
• In dihedral the element data_type is used to specify the type of data CSI or TALOS.
• Symmetry is used when the molecule is treated as a symmetric multimer. The element method specify the method that ensures the symmetry, currently only method is implemented “Standard”: symmetry-ADR (Nilges, Proteins, 1993). The element symmetry_type specifies the type of symmetry, C2, C3, C5, D2.
• If ncs_enabled is “yes”, NCS restraints are applied to minimize the RMSD between monomers during the refinement.
• If packing_enabled is “yes”, the packing restraints are applied to keep the monomers close to each-other. If you think you have enough inter-monomer restraints, just disable.

• To force the use of a given structure in place of the extended structure generated by CNS, as a starting point for the calculation, for example, in the case, one wants to filter NOE data with respect to a given already known structure, on can use the attribute 'file' in the element initial_structure.
  

• section cns:
  

<cns local_executable="/Bis/shared/cns/intel-i686-linux/bin/cns_solve" 
   keep_output="yes" keep_restraint_files="yes" create_psf_file="yes" 
   generate_template="yes" nonbonded_parameters="PROLSQ"> 
  <annealing_parameters> 
    <unambiguous_restraints first_iteration="0" 
     k_hot="10.0" k_cool1_initial="10.0" k_cool1_final="50.0" k_cool2="50.0"/> 
    <ambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
       k_cool1_final="50.0" k_cool2="50.0"/> 
    <hbond_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
       k_cool1_final="50.0" k_cool2="50.0"/> 
    <dihedral_restraints k_hot="5.0" k_cool1="25.0" k_cool2="200.0"/> 
    <karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="4" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <karplus_restraints parameter_class="5" a="6.98" b="-1.38" c="1.72" 
       d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
    <rdc_restraints parameter_class="1" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="2" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="3" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="4" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <rdc_restraints parameter_class="5" method="SANI" first_iteration="0" 
       k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" 
       border_hot_initial="0.1" border_hot_final="40.0" 
       border_cool1_initial="40.0" border_cool1_final="40.0" 
       border_cool2_initial="40.0" border_cool2_final="40.0" 
       center_hot_initial="0.1" center_hot_final="0.1" 
       center_cool1_initial="10.0" center_cool1_final="10.0" 
       center_cool2_initial="10.0" center_cool2_final="10.0"/> 
    <flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" 
       m_rswitch_cool2="0.5" rswitch_hot="0.5" rswitch_cool1="0.5" 
       rswitch_cool2="0.5" m_asymptote_hot="-1.0" m_asymptote_cool1="-1.0" 
       m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" 
       asymptote_cool2="0.1"/> 
    <symmetry_restraints k_packing_cool2="5.0" last_iteration_packing="8"
        k_ncs="50.0"k_packing="1.0" k_ncs="50.0"/>
    <logharmonic_potential enabled="yes" use_auto_weight="yes" weight_unambig="1.0"
        weight_ambig="1.0" weight_hbond="1.0"/>
  </annealing_parameters> 
  <md_parameters dynamics="torsion" random_seed="89764443" 
    tad_temp_high="10000.0" tad_timestep_factor="9.0" 
    cartesian_temp_high="2000.0" cartesian_first_iteration="0" 
    timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" 
    steps_high="25000" steps_refine="4000" steps_cool1="20000" 
    steps_cool2="20000"/> 
</cns>

• The CNS simulated annealing protocol contains one hot stage and two cooling stages, and the corresponding attributes contain the substrings 'hot', 'cool1' and 'cool2'.
  
• The attribute local_executable contains the complete path of the cns binary used for the cns set-up (generation of psf files, of extended structures).  Other attributes describes whether the CNS output files are kept (they may be very large files), whether the restraint .tbl files generated for CNS are kept, and  whether the initial psf (parameter file of the analyzedmolecular system) and template files should be generated. The type of non-bonded parameters used during the calculation is described using the attribute 'nonbonded_parameters'. This attribute can have the values: 'PROLSQ',  'PARMALLH6', 'PARALLHDG' and 'OPLSX' (look at Linge and Nilges (1999) J Bio NMR in the list of references).
  
• The elements unambiguous_restraints, ambiguous_restraints and hbond_restraints describe the simulated annealing set-up for the distance restraints: the  force constants during the different steps of the simulated annealing are the attributes k_*. The attribute first_iteration gives the iteration number from which the corresponding restraint is applied.
  
• The elements dihedral_restraints, karplus_restraints and rdc-restraints describe the set-up for the angular restraints. Karplus restraints and rdc (residual dipolar coupling) restraints can be grouped into classes. Every class has its own parameter set which the user has to specify. It contains the specification of the alignment tensor for the rdcs and settings for the simulated annealing protocol.
• The attribute method in the element rdc-restraints describes the approcah to use rdc data. ARIA offers two approaches to use residual dipolar coupling data as restraints: SANI and VEAN. For SANI, you have to specify the rhombicity and magnitude of the alignment tensor. VEAN uses angular restraints which must be precalculated with a separate program.
  
• The element flat_bottom_harmonic_wall describes the shape of the restraint potential.
  
• The  element symmetry_restraints contains the force constant for the packing term (k_packing_hot k_packing_cool1 and k_packing_cool2 ) and for the non-crystallographic symetry (k_ncs). 

• You can use the new potential (log-harmonic potential) in replacement of the soft square potential. If use_auto_weight is set to “yes”, the distance restraints weight for the log-harmonic potential are automatically calculated, otherwise you can specify them in the elements weight_unambig, weight_ambig, weight_hbond. If you use the log-harmonic potential, please quote the following reference: Nilges M., Bernard A., Bardiaux B., Malliavin T.E., Habeck M., Rieping W. (2008) Accurate NMR structures through minimization of an extended hybrid energy. Structure 16,9:1305-1312.

• The element md_parameters contains the molecular dynamics parameters describing the simulated annealing protocol. The attribute dynamics is equal to "torsion" in the torsion angle dynamics is used in the high temperature and cooling stages, and is equal to cartesian if no torsion angle dynamics is used. The temperature values are the attributes *_temp_* and the number of integration steps are the attributes steps_*.
  

• section job_manager:

<job_manager default_command="csh -f">
  <host enabled="yes" 
    submit_command="glite-wms-job-submit -a"
    state_command= "glite-wms-job-status"
    output_command= "glite-wms-job-output --dir"
    executable="/Bis/shared/centos-3/cns_solve-1.1_20041015_intel-8.1_x86/intel-i686-linux/bin/cns_solve" n_cpu="50" use_absolute_path="yes"/> 
</job_manager>

• In the element job_manager, three values of the attribute default_command are possible "LOCAL", "CLUSTER", "GRID" to specify the computing mode:
• LOCAL to calculate on the local computer.
  • The element host contains the parameters related to the generation of conformers on the computer. The attribute submit_command is used to specify the command csh -f or default.
• CLUSTER to calculate on a cluster :
  • The element host contains the parameters related to the generation of conformers on several computers: 'enabled' is the option to enable a given host. The attribute submit_command describes how to launch a job on the given host. Two possibilities are given in the example above: use the batch system SGE, or a simple ssh command to the host. In the first case, no hostname should be given, as sge is dispatching the CPU time between the users. The attribute executable: The absolute path of the CNS binary on the given host. WARNING: if you are using qsub or another batch system dispatching automatically the CPU time between the users, as you are not giving any hostname, the absolute path should be the same on all the computers you will use. Two ways to do so are: (i) install cns on disk exported to all computer, (ii) have exactly the same cns installation on each computer.

• GRID to calculate on a grid :
  • The element host contains the parameters related to the generation of conformers on the grid computers with commands necessary to manage the CNS jobs. If the grid work with the middleware glite, you can used default as commands for attributes submit_command, state_command and output_command. By default commands are : glite-wms-job-submit -a, glite-wms-job-state, glite-wms-job-output –dir.
• By example, if all calculations are run on the local computer, the syntax is:

<job_manager default_command="LOCAL">
  <host enabled="yes"
     submit_command="csh -f"
     state_command= ""
     output_command= ""
     executable="/Bis/shared/centos-3/cns_solve-1.1_20041015_intel-8.1_x86/intel-i686-linux/bin/cns_solve" n_cpu="2" use_absolute_path="yes"/>
</job_manager>

• section protocol:

<protocol floating_assignment="yes"> 
  <iteration number="0" n_structures="40" sort_criterion="total_energy" n_best_structures="7" n_kept_structures="0"> 
    <assignment/> 
    <merging method="no_merging"/> 
    <calibration relaxation_matrix="no" distance_cutoff="6.0" 
      estimator="ratio_of_averages" error_estimator="distance"/> 
    <violation_analysis violation_tolerance="1000.0" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="1.0" max_contributions="20"/> 
    <network_anchoring high_residue_threshold="4.0" enabled="yes" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
      v_min="0.1"/> 
  </iteration>
............................................................
  <iteration number="8" n_structures="100" sort_criterion="total_energy" n_best_structures="7" n_kept_structures="0"> 
    <assignment/> 
    <merging method="no_merging"/> 
    <calibration relaxation_matrix="no" distance_cutoff="6.0" 
      estimator="ratio_of_averages" error_estimator="distance"/> 
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="0.8" max_contributions="20"/> 
    <network_anchoring high_residue_threshold="4.0" enabled="yes" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
  </iteration> 
  <water_refinement solvent="water" n_structures="10" enabled="yes" write_solvent_molecules="no"/> 
</protocol>

• The attribute floating_assignment describes whether the floating chirality assignment is used (equivalent hydrogens are swapped and the energy difference is measured): floating_assignment can take the values "yes" or "no".    It is often difficult to assign the chemical shifts of the two substituents of a prochiral center stereospecifically. In proteins, these are the two methylene protons or the methyl protons of the isopropyl groups of valine or leucine. A resonance matching one of the chemical shifts in the proton dimensions potentially involves either of the two prochiral substituents. ARIA compensates this lack of information by testing both alternatives during structure calculation. For each calculated structure, the energetically preferred options are written to a file witha .float extension (see the page Results analysis). 

• Parameters specific for each iteration are contained in the element iteration.The total number of generated structures is given by n_structures, only the number of selected structure for assignment statistics is given by n_best_structures of structures. The criterion for sorting is according the total energy, which is the only possible value for the attribute sort-criterion. You can also specify the number of structures kept from the previous iteration (n_kept_structures). These structures do not undergo the high temperature stage of the molecular dynamics.

• The element merging describes how the number of peaks can be reduced by merging: the attribute method can be equal to "standard" (peaks with the same assignment are merged), "no_merging" (no peak merging) or "combination" (only for versions 2.2 and later: it is equivalent to the "restraint combination" in CYANA, two long-range peaks are merged in one peak).
  
• The element calibration describes the way the experimental peak intensities measured from spectra are calibrated with respect to the theoretical peak intensities calculated from the set of conformers. The attribute relaxation_matrix is present only in versions 2.2 and later, and says whether the calibration is done by calculating the intensities from the relaxation matrix. The attribute estimator defines how the calibration of experimental intensity with respect to the calculated ones is performed. The defalut value "ratio_of_averages" corresponds to a calibration through the ratio of the average experimental and calculated intensities/volumes and is the only possible value for the moment. The attribute distance_cutoff is used to filter the calculated intensities/volumes used for the calibration by including only those corresponding to a distance smaller than the distance_cutoff value. If no value is given, all crosspeaks are considered. The attribute  error_estimator is active only in case of spin diffusion correction (relaxation_matrix="yes") and is present in versions 2.2 and later. It can be equal to "distance" or to "volume": in the first case, the error used to calculate the corrected lower and upper bounds, is estimated from the distance target, or from the back-calculated intensity. If relaxation_matrix="no", the distance target is used.
  
• In the element violation_analysis, the attribute violation_tolerance is the limit of distance value for which a restraint is not considered as violated. This value decreases during the simulated annealing iterations. The violated restraints are those for which the distance is larger than the sum of the upper bound limit and of the attribute violation_threshold. 
• In the element partial_assignment, the attribute weight_threshold a weight which is assigned to every contribution by the 'Partial Assignment' step. The sum of weights over all contributions in a restraint is always greater or equal to the attribute 'weight_threshold'. The attribute 'max_contributions' gives the maximum number of contributions possible for a given ARIA peak.
• The element network_anchoring is present in version 2.2 of ARIA and in later versions.
• The element water_refinement describes the features of the final refinement step in solvent. The refinement is enables through the attribute 'enabled'. The solvent is given by the attribute 'solvent' (default value: "water", other possible value: "dmso"). The number of refined structures is given by the attribute 'n_structures', and the PDB files will include solvent molecules if the attribute 'write_solvent_molecule' is 'yes'.

• section analysis:
  

<analysis> 
  <structures_analysis enabled="yes"/> 
  <procheck executable="/Bis/shared/centos-3/bin/procheck" enabled="yes"/> 
  <prosa executable="prosa" enabled="no"/> 
  <whatif executable="/Bis/shared/bin/whatif.intel-7.1" enabled="yes"/> 
</analysis>

• The element structures_analysis enables or disables, with the attribute enable, the analysis of the final structures.
• The elements procheck, prosa and whatif enable or disable the use of the corresponding softwares for the final structures analysis: the attributes executable contain the full path of the software executable.
  

• section report:
  

<report>
  <ccpn enabled="no"/>
  <molmol enabled="yes"/>
  <noe_restraint_list pickle_output="no" text_output="yes" xml_output="yes"/><report> 
  <ccpn export_noe_restraint_list="no" export_structures="yes"/> 
</report>

• The element ccpn describes whether ARIA exports the complete project (last iteration) as CCPN XML files. The attributes export_noe_restraint_list and export_structures describe whether the noe restraint list and/or the structures are exported.
  
• The element molmol tells whether a molmol script is produced, if the attribute 'enabled' of the section 'molmol' is equal to "yes".
• In the element noe_restraint, an assigned NOE restraint list can be produced, in a python binary format (attribute 'pickle_output'), in a test format (attribute 'text_output') or in a xml format (attribute 'xml_output').
• The element spectra describes the output of an assigned peak list in the xml format of ARIA. The attribute write_assigned tells whether the assigned peak list should be written or not.  The attribute write_assigned_force tells whether already existing peak lists should be erased by the new output. The attribute iteration tells whether the assigned peak list should be written at each iteration ("all") or only at the last one ("last").
  

Example of file

An example of a generic project file is given below, in a format compatible with the version 2.1 of ARIA. For specific applications of ARIA, please have a look to the tutorial introduction page:

<!DOCTYPE project SYSTEM "project1.0.dtd">
<project name="" version="1.0" author="" date="" description="" comment="" references="" 
working_directory="/home/Bis/terez/ARIA/test" temp_root="/home/Bis/terez/ARIA/test" 
run="1" file_root="my_molecule" cache="yes" cleanup="yes">
<data>
  <ccpn_model filename=""/>
  <molecule file="./xml/hrdc.xml" format="xml">
    <linkage_definition name="automatic" filename=""/>
    <parameter_definition name="automatic" filename=""/>
    <topology_definition name="automatic" filename=""/>
  </molecule>
  <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no">
    <shifts file="./xml/13C_ppm.xml" format="xml" default_shift_error="0.0"/>
    <peaks file="./xml/13C_noe.xml" format="xml" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" freq_window_proton2="0.02" freq_window_hetero2="0.5"> ]]>
      <lower_bound_correction value="0.0" enabled="no"/> 
      <upper_bound_correction value="6.0" enabled="no"/>
    </peaks>
  </spectrum> 
.................................
  <initial_structure file="" format="iupac" enabled="no"/>
</data>
<structure_generation engine="cns">
  <cns local_executable="" keep_output="yes" keep_restraint_files="yes" create_psf_file="yes" 
     generate_template="yes" nonbonded_parameters="PROLSQ">
    <annealing_parameters>
      <unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
         k_cool1_final="50.0" k_cool2="50.0"/>
      <ambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
         k_cool1_final="50.0" k_cool2="50.0"/>
      <hbond_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
         k_cool1_final="50.0" k_cool2="50.0"/> 
      <dihedral_restraints k_hot="5.0" k_cool1="25.0" k_cool2="200.0"/>
      <karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
      <karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> 
      <karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> ]]> 
      <karplus_restraints parameter_class="4" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/> ]]>
      <karplus_restraints parameter_class="5" a="6.98" b="-1.38" c="1.72" d="-60.0" 
         k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
      <rdc_restraints parameter_class="1" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="2" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="3" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="4" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <rdc_restraints parameter_class="5" method="SANI" first_iteration="0" k_hot="0.0" 
         k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" 
         border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" 
         border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" 
         center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" 
         center_cool2_initial="10.0" center_cool2_final="10.0"/>
      <flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" m_rswitch_cool2="0.5" 
         rswitch_hot="0.5" rswitch_cool1="0.5" rswitch_cool2="0.5" m_asymptote_hot="-1.0" 
         m_asymptote_cool1="-1.0" m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" 
         asymptote_cool2="0.1"/>
    </annealing_parameters>
    <md_parameters dynamics="torsion" random_seed="89764443" tad_temp_high="10000.0" 
       tad_timestep_factor="9.0" cartesian_temp_high="2000.0" cartesian_first_iteration="0" 
       timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" steps_high="10000" 
       steps_refine="4000" steps_cool1="5000" steps_cool2="4000"/>
  </cns>
  <job_manager default_command="csh -f"/>
</structure_generation>
<protocol floating_assignment="yes">
  <iteration number="0" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1000.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="1.0" max_contributions="20"/>
  </iteration>
  <iteration number="1" n_structures="20" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="5.0" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="0.9999" max_contributions="20"/>
  </iteration>
  <iteration number="2" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="3.0" violation_threshold="0.5"/> 
    <partial_assignment weight_threshold="0.999" max_contributions="20"/>
  </iteration> 
  <iteration number="3" n_structures="20" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.99" max_contributions="20"/>
  </iteration>
  <iteration number="4" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.98" max_contributions="20"/>
  </iteration>
  <iteration number="5" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.96" max_contributions="20"/>
  </iteration>
  <iteration number="6" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.93" max_contributions="20"/>
  </iteration>
  <iteration number="7" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.9" max_contributions="20"/>
  </iteration> 
  <iteration number="8" n_structures="20" sort_criterion="total_energy" n_best_structures="7"> 
    <assignment/>
    <merging method="standard"/>
    <calibration estimator="ratio_of_averages" distance_cutoff="6.0"/>
    <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
    <partial_assignment weight_threshold="0.8" max_contributions="20"/>
  </iteration>
  <water_refinement solvent="water" n_structures="10" enabled="yes" write_solvent_molecules="no"/>
</protocol>
<analysis>
  <structures_analysis enabled="yes"/>
  <procheck executable="procheck" enabled="yes"/<prosa executable="prosa" enabled="yes"/>
  <whatif executable="whatif" enabled="yes"/>
</analysis>
  <report>
    <ccpn export_assignments="yes" export_noe_restraint_list="no" export_structures="yes"/>
    <molmol enabled="yes"/>
    <noe_restraint_list pickle_output="yes" text_output="yes" xml_output="no"/>
    <spectra write_assigned="yes" write_assigned_force="yes" iteration="last" write_unambiguous_only="no"/>
</report>
</project>