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.