Using RotamerConvolveMD

When installing the package, two scripts are installed in the bin directory:

  • convolve-mtss-rotamers.py analyzes standard DEER experiments with MTSL spin labels.

  • convolve-mtss-rotamers_pre.py analyzes PRE experiments with MTSL spin labels.

Scripts are run from the command line.

DEER

Analysis for standard DEER experiments with MTSL spin labels is performed with the script convolve-mtss-rotamers.py. It takes as input

  • a topology or structure file (psf, gro, pdb, … any topology format recognized by mdanalysis)

  • a trajectory (dcd, xtc, trr, … any trajectory format that mdanalysis can read)

A typical invocation:

convolve-mtss-rotamers.py \
    --resid 47 330  \
    --histogramBins 0 80 1  \
    --clashDistance 2.2  \
    --output "dat/peptso-xrd" \
    --plotname "dat/peptso-xrd.pdf" \
    --outputRawDistances "dat/peptso-xrd" \
    --dcdfilename "dcd/peptso-xrd" \
    --dcdfilenameNoClashes "dcd/peptso-xrd" \
    --useNOelectron \
    peptso.gro peptso.xtc

It loads the MD trajectory from the topology peptso.gro and the trajectory peptso.xtc. The --resid pair is required and denotes the residue numbers (in the topology) to which the MTSSL spin labels would be attached. Rotamers that overlap with protein atoms as measured by an atom-atom distance smaller than the --clashDistance will be discarded and not counted in the distance calculations. The user can decide to use either N1 --useNOelectron or the geometric midpointis N1 and O1 --no-useNOelectron to calculate the distances. For further explanations see the --help option.

For an example, see doc/example in the source distribution. The example can also be run to test the installation as reference output is provided.

PRE

Analysis for standard PRE experiments with MTSL spin label is performed with the script convolve-mtss-rotamers_pre.py. Similar to the analysis of DEER experiments, it takes as inputs:

  • a topology or structure file (psf, gro, pdb, … any topology format recognized by mdanalysis)

  • a trajectory (dcd, xtc, trr, … any trajectory format that mdanalysis can read)

A typical invocation:

convolve-mtss-rotamers_pre.py \
    --resid 47  \
    --clashDistance 2.2  \
    --plotname "dat/peptso-xrd-47.pdf" \
    --outputRawDistances "dat/peptso-xrd" \
    --dcdfilenameAll "dcd/peptso-xrd" \
    --dcdfilenameNoClashes "dcd/peptso-xrd" \
    --useNOelectron \
    peptso.gro peptso.xtc

The --resid is required and denotes the residue number (in the topology) to which the MTSSL spin label would be attached. Rotamers that overlap with protein atoms as measured by an atom-atom distance smaller than the --clashDistance will be discarded and not counted in the distance calculations. The user can decide to use either N1 --useNOelectron or the geometric midpointis N1 and O1 --no-useNOelectron to calculate the distances. For further explanations see the --help option.