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joaomcteixeira edited this page Aug 23, 2017 · 38 revisions

Warnings, Errors and Troubleshooting (WET) list

  1. The PRE Analysis flag is set to True but other flags upon which it fully or partially depends are set to False. a. PRE Analysis is only performed over the analysis of condition 3 (z axis), if this flag (do_cond3) is set to False, PRE Analysis won't be performed. b. PRE Analysis is performed on Height and/or Volume ratio calculations, at least one of those flags should be set True. c. DELTA_PRE Oscilation maps are only performed on Comparisons, Perform Comparisons should True for this plot to be printed.

  2. No analysis is activated. Farseer performs analysis on three different dimensions (conditions) of the input dataset, nevertheless, those analysis routines need to be activated in the farseer_user_variables file using variables do_cond1, do_cond2 and do_cond3. If all those variables are set to False, parsed peaklists with lost and unassigned residues identified will be exported but no calculation or plot representation will be performed

  3. No plots activated. Farseer allows the user to configure which parameters are calculated and from those, which kind of plots are drawn. When no plots are turned ON Farseer will export only the calculated parameters.

  4. Input x values for restraints fitting do not match data points for condition 1. Farseer allows fitting of the calculated restraints to specific equations, nevertheless, fitting is only allowed along the condition 1 data points. For fitting to be performed Farseer requires the user to input a list of values that correspond to the experimental values to be used in as x values in the fitting equation. For example, fitting a CSPs evolution to an increasing ligand concentration requires fitting_x_values variable to be a list of the experimentally investigated ligand concentrations. The number of input values has to match the number of peaklist (.csv files) along condition 1 and if condition 1 .csv file names can be converted to number values, those have to match the fitting_x_values variable.

  5. Number of input x values (coordinate axis) do not match the number of input peaklists. Farseer allows fitting of the calculated restraints to specific equations, nevertheless, fitting is only allowed along the condition 1 data points. For fitting to be performed Farseer requires the user to input a list of values that correspond to the experimental values to be used in as x values in the fitting equation. For example, fitting a CSPs evolution to an increasing ligand concentration requires fitting_x_values variable to be a list of the experimentally investigated ligand concentrations. The number of input values has to match the number of peaklist (.csv files) along condition 1, where 0 relates to the reference experiment (peaklist). Even if fitting is disabled, fitting_x_values can be used for Residue Evolution Plot if res_evo_set_x_values flag, fitting_x_values has to match number of peaklists input.

  6. There are negative values in titration_x_values variable. Farseer has implemented fitting only to the Hill Equation (http://www.physiologyweb.com/calculators/hill_equation_interactive_graph.html) which does not consider the use of negative values in the coordinate axis. Please correct your input data in titration_x_values variable.

  7. x values given by the user for fitting look good. This is not an error nor a warning, it's just an alert to the user about the values used in as x coordinates to perform the fitting.

  8. Files are missing in the input folder tree. Farseer assumes that when analysing different titrations together, those are related. Therefore the same number of files (data points) should be given for every condition. For example, there should be the same number of peaklists (.csv files) in each subfolder, as well as the same subfolder tree should be maintained under spectra/.

  9. There are no files of the . You have asked Farseer-NMR to read a certain file type that does not exist in the spectra/ folder.

  10. File names do not match. File names corresponding to the X data points, for example, peaklists .csv files, MUST have the same name in all the y data point folders. Even if files reffer to different concents, names should be normallized to be the same. For example:

    WRONG!
     298/
        M1/
            M1_L1_1.csv
            M1_L1_2.csv
     298/
        M2/
            M2_L1_1.csv
            M2_L1_2.csv
     RIGHT!
     298/
        M1/
            L1_1.csv
            L1_2.csv
     298/
        M2/
            L1_1.csv
            L1_2.csv
  1. Folder names do not match. Folder names corresponding to the Y data points (for example peaklists .csv files) MUST have the same name in all the Z data point folders. For example:
    WRONG!
     298/
        298_M1/
            L1_1.csv
            L1_2.csv
     278/
        278_M1/
            L1_1.csv
            L1_2.csv
     RIGHT!
     298/
        M1/
            L1_1.csv
            L1_2.csv
     278/
        M1/
            L1_1.csv
            L1_2.csv

  1. .fasta files are missing in the input folder tree. If Apply FASTA variable is set to True, a .fasta file must exist in each Y axis folder. Farseer-NMR found that some .fasta files are missing while others are present. Please look for those missing.

  2. Nothing to do with these files. File type you tried to read is not compatible with Farseer-NMR. There's nothing to be done with those files. Please select a compatible file type: .csv or .fasta.

  3. Empty Data points. Farseer-NMR as detected an empty data point in the peaklist files. If you want to add an empty data point from a missing value, please add the header followed by a 'new line' character to that same file. Use the following header: Assign F1,Assign F2,Merit,Details,Fit Method,Vol. Method,Number,#,Position F1,Position F2,Height,Volume,Line Width F1 (Hz),Line Width F2 (Hz)

  4. Missing tag position. The tag position should be writen as header of the *.pre file containing the information on theoretical PRE data. Header format should be, e.g. residue 40: #40.

  5. Unexistent reference residue. The residue you have selected to use as reference for chemical shift correction does not exist or is unassigned or lost. Select a valid residue in the Settings Menu or confirm the usage flag is not activated by mistake.

  6. Unexistent tag residue. The residue selected for the tag position in the *.pre file, for theoretical PRE, is not part of the protein sequence.

  7. The .fasta file is shorted than the reference experiment. Is you have input a FASTA file containing the whole protein sequence, with the intent of identifying the unassigned residues, it is expected that the .fasta file has more residue entries than the reference experiment of that series. This is not the case. Confirm that the .fasta file is correct.

  8. Comparing references that do not exist. The flags expand_lost_yy or expand_lost_zz are activated in the Run Settings. Though, there are is only one datapoint along these axis and, therefore, nothing to compare with. Leaving the flag active won't affect the calculation, though you might want to deactivate it.

  9. Calculation along axis is activated but there are no data points. You have activated a calculation axis flag (x, y or z) but there are no data points along that given axis. The flag may be activated by mistake.

  10. Different .fasta sizes incompatibility. .fasta files must have the same size, that is, number of rows/residues when analysing Series along the Y axis (which is the axis that receives the .fasta files). Read further on axes restrictions.

  11. FASTA file contains number in between the protein's primary sequence. What else needs to be said? :-)

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