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:** .. code-block:: bash 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:** .. code-block:: bash -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 ------- .. code-block:: bash 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: .. code-block:: bash xmgrace -settype xydy deformation.dat The obtained plot is similar to the second plot `shown here <../notebooks/base_steps_tutorial.html#Deviation-in-parameters-of-bound-DNA-with-respect-to-free-DNA>`_ for bound DNA.