localDeformation

Deformation of local parameters in probe DNA with respect to a reference DNA

This can be used to calculate deformation in the given parameters of a probe DNA with respect to a reference DNA along the base-pairs/steps.

Note

Number of input segments/bp/bps should match between probe and reference DNA. It means ([-bePrb] - [-bsPrb]) should be equal to ([-beRef] - [-bsRef]).

Usage:

usage: dnaMD localDeformation [-h] [-ir L-BP_fdna.dat] [-ip L-BP_cdna.dat]
                              [-o output.dat] [-oxb ref]
                              [-tbpPrb total-bp-number]
                              [-tbpRef total-bp-number] [-p parameter]
                              [-em block] [-mb bp/s number] [-gt g_analyze]
                              [-bsPrb bp/s-start-number]
                              [-bePrb bp/s-end-number]
                              [-bsRef bp/s-start-number]
                              [-beRef bp/s-end-number] [-mm sum-or-mean]
                              [-fbpPrb 1] [-fbpRef 1]

Optional arguments:

-h, --help            show this help message and exit
-ir L-BP_fdna.dat, --input-reference L-BP_fdna.dat
                    Name of input file for reference DNA (from do_x3dna or hdf5 file).
                    This file should contain the required parameters. It can be a file either
                    produced from do_x3dna or hdf5 storage file.

-ip L-BP_cdna.dat, --input-probe L-BP_cdna.dat
                    Name of input file for probe DNA (from do_x3dna or hdf5 file).
                    This file should contain the required parameters. It can be a file either
                    produced from do_x3dna or hdf5 storage file.

-o output.dat, --output output.dat
                    Name of output file.
                    The extracted output will be written in output file.

-oxb ref, --xaxis-bp-source ref
                     Basepair/step number on the x-axis in output file
                    To write the base-pair/step number of either probe or reference DNA in the output file.

                    If base-pair numbering is different in reference and probe DNAs, then this option can be used to
                    write the base-pair number of either probe (-oxb probe) or reference (-oxb ref) DNA in the output file.

-tbpPrb total-bp-number, --total-bp-probe total-bp-number
                    Total number of basepair in probe DNA.
                    It is an essential input.

-tbpRef total-bp-number, --total-bp-Ref total-bp-number
                    Total number of basepair in reference DNA.
                    It is an essential input.

-p parameter, --parameter parameter
                    Parameter name.
                    This parameter will be extracted from file. Ensure that parameter is present
                    in the file, otherwise wrong values will be extracted from file.

-em block, --error-method block
                     Error method
                    It can be as following:
                    * "acf": Using autocorrelation function to determine autocoprrelation time and used as time
                             to get the independent frame.
                    * "block": Block averaging error
                    * "std": standard deviation

                    In case of "acf" and "block", gromacs tool "g_analyze" or "gmx analyze" will be used. Either
                    of these tools should be in path for error calculation.

-mb bp/s number, --merge-bps bp/s number
                    Number of consecutive base-pairs/steps to merge for creating the small non-overlapping DNA
                    segments. By default, averages and errors are calculated for each base-pair/step separately.
                    However, averages  and errors can also  be calculated for small non-overlapping DNA segment
                    by merging the parameters of consecutive base-pairs/steps.

-gt g_analyze, --gromacs-tool g_analyze
                    Tools to calculate autocorrelation time or bloack averaging error.
                    By default it is g_analyze (Gromacs-4.5.x/4.6.x versions). For newer versions, use "gmx analyze".

-bsPrb bp/s-start-number, --bp-start-probe bp/s-start-number
                    First BP/BPS of probe DNA after which parameter will be extracted.
                    If it is not given, first basepair or base-step will be considered.

-bePrb bp/s-end-number, --bp-end-probe bp/s-end-number
                    Last BP/BPS of probe DNA upto which parameter will be extracted.
                    If it is not given, last basepair or base-step will be considered.

-bsRef bp/s-start-number, --bp-start-ref bp/s-start-number
                    First BP/BPS of reference DNA after which parameter will be extracted.
                    If it is not given, first basepair or base-step will be considered.

-beRef bp/s-end-number, --bp-end-ref bp/s-end-number
                    Last BP/BPS of reference DNA upto which parameter will be extracted.
                    If it is not given, last basepair or base-step will be considered.

-mm sum-or-mean, --merge-method sum-or-mean
                    Method to merge the parameters of consecutive basepairs/steps given by -mb/--merge-bps.

                    Currently accepted keywords are as follows:
                        * mean : Average of local parameters
                        * sum : Sum of local parameters

-fbpPrb 1, --first-bp-probe 1
                    Basepair number of first base-pair in probe DNA.
                    Usually it is one. Therefore, if this option is not provided, base-pair
                    numbering will start from one.

-fbpRef 1, --first-bp-ref 1
                    Basepair number of first base-pair in reference DNA.
                    Usually it is one. Therefore, if this option is not provided, base-pair
                    numbering will start from one.

Example

dnaMD localDeformation -ir pdna.h5 -ip fdna.h5 -o deformation.dat -tbpPrb 60 -tbpRef 60 -bsPrb 5 -bePrb 56 \
-bsRef 5 -beRef 56 -mm sum -mb 4 -em block -p shift -gt "gmx analyze"

Following output is obtained in deformation.dat file.

# bp(mid)    shift-avg       shift-error
7           0.0539361       0.0486333
11          0.122707        0.0485817
15          0.206374        0.269953
19          -0.0630569      0.228433
23          -0.535754       0.247015
27          0.697832        0.253653
31          -0.453067       0.0476092
.
.
.

It can be plotted by xmgrace as following:

xmgrace -settype xydy deformation.dat

The obtained plot is similar to the second plot shown here for bound DNA.