trace_plot

Reliability status: development

script to plot one or multiple traces in 3D

Takes a trace file and either:

• ranks traces and plots a selection

• plots a user-selected trace in .ecsv (barcode, xyz) and PDF formats. The output files contain the trace name.

• saves output coordinates for selected traces in pdb format so they can be loaded by other means including https://www.rcsb.org/3d-view, pymol, or nglviewer.

future:

• output PDBs for all the traces in a trace file

usage: trace_plot [-h] [--input INPUT] [-n NUMBER_TRACES] [-N N_BARCODES]
                  [--selected_trace SELECTED_TRACE]
                  [--barcode_type_dict BARCODE_TYPE_DICT] [--all] [--pipe]
                  [-O OUTPUT]

Named Arguments

--input

Name of input trace file.

-n, --number_traces

Number of traces treated

-N, --N_barcodes

minimum_number_barcodes. Default = 2

--selected_trace

Selected trace for analysis

--barcode_type_dict

Json dictionary linking barcodes and atom types (MUST BE 3 characters long!).

--all

plots all traces in trace file

Default: False

--pipe

inputs Trace file list from stdin (pipe)

Default: False

-O, --output

Tag to add to the output file. Default = filtered

Examples

$ ls Trace_3D_barcode_KDtree_ROI:1.ecsv | trace_plot --pipe --selected_trace 5b1e6f89-0362-4312-a7ed-fc55ae98a0a5

this pipes the file ‘Trace_3D_barcode_KDtree_ROI:1.ecsv’ into trace_plot and then selects a trace for conversion.

$ trace_plot --input Trace_3D_barcode_KDtree_ROI:1.ecsv --all

this plots all traces in the trace file.

Format for json dict

Please use the following format for the json dictionary to link barcode identities with different ATOM names in the PDB file:

{"12": "C  ", "18": "C  ", "9": "P  "}

keys provide barcode names in the trace file, these should be attributed to 3 character codes

pymol

Some useful pymol commands:

set grid_mode,1
color green,  (name C*)
color red, (name P*)