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.