BFMP Tutorial 2

Determining the ring conformation of Iduronic acid from a PDB file using BFMP.

If needed, please click here for instructions on downloading and installing the BFMP program.

The program requires two input files: a text file in PDB format and a configuration file.

  1. Click here to download BFMP-Tutorial2.tar.gz, the input and output files for this tutorial
  2. Using vi or any text editors open the text file (the configuration file) called input.txt containing the following information:
  3. Each of the three keywords shown in the file above should be followed on subsequent lines by the relevant values as described below in the same order as specified above. For detailed descriptions of these parameters, please read the Documentation available here.
    • Atom: The ring atom names, in order around the ring starting from the first atom. For an aldohexapyranose, the list should begin with the anomeric carbon, with the other ring atoms listed in order moving towards the ring oxygen.
    • Residue: The number of the residue containing the ring whose conformation should be analyzed. In this case we want to analyze residue # 506 which is an Iduronic acid.
    • Cut off:  A cut off value of 10° is specified here.  The user can alter this value.  If it is larger, a larger number of structures will be categorized as IUPAC.  If smaller, then fewer will.
    • Path: The path to the text file which is required to run the program. Please edit this path to match the path to your canonical.txt file which was provided when you downloaded the software.
  4. Run the program.
    /path/to/your/detect_shape 1AXM.pdb input.txt

    Note: According to /usr/bin/time, this command took less than 0.2 s to run on an Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz processor. If you have a similar or faster processor, and it takes much longer than that, something might have gone wrong.  The output file, ring_conformations.txt, should contain two lines.

  5. Check the analysis output
    • If desired, you can compare the output you get to output files we created.  Please note that these files can be compared only if used a 10° cutoff value. If you used a different cut off value they might no longer be comparable. To make the comparison, the “diff” command should do, and, if successful, should give the following output:
      % diff -s ring_conformations.txt ring_conformations_Tutorial-2.txt
      Files ring_conformations.tx and ring_conformations_Tutorial-2.txt are identical
    • The output file has three columns. For example, this might be a line in the file:
      1    -    3d6(1.278024)   5d2(9.817732)

      This indicates that the there are two best fit four-membered planes below the cut off values specified (10°).  The positions of the out of plane atoms of these two planes also indicate that this conformation is distorted and cannot be well described using standard IUPAC nomenclature. This is indicated using “-” in the second column.

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