As of v2.1, I’ve switched from Perl to Ruby as the scripting language for 3DNA. Consequently, the Perl scripts in previous versions of 3DNA (v1.5 and v2.0) are now obsolete. I’ll only correct bugs in existing Perl scripts, but will not add any new features.
For back reference, the scripts are still available from a separate directory $X3DNA/perl_scripts, with the following contents:
OP_Mxyz* dcmnfile* nmr_strs* README del_ms* pdb_frag* block_atom* expand_ids* x3dna2charmm_pdb* blocview.pl* manalyze* x3dna_r3d2png* bp_mutation* mstack2img* x3dna_setup.pl* cp_std* nmr_ensemble* x3dna_utils.pm
Among them, x3dna_setup.pl and blocview.pl have corresponding Ruby versions: x3dna_setup and blocview. Actually, the .pl file extension (for Perl) was added to avoid confusion with the new Ruby scripts.
Some of the functionalities have been incorporated into the Ruby script x3dna_utils:
------------------------------------------------------------------------
A miscellaneous collection of 3DNA utilities
Usage: x3dna_utils [-h|-v] sub-command [-h] [options]
where sub-command must be one of:
block_atom -- generate a base block schematic representation
cp_std -- select standard PDB datasets for analyze/rebuild
dcmnfile -- remove fixed-name files generated with 3DNA
x3dna_r3d2png -- convert .r3d to image with Raster3D or PyMOL
------------------------------------------------------------------------
--version, -v: Print version and exit
--help, -h: Show this message
Along the same line, ensemble-related functionalities (for NMR or molecular dynamics simulations) have been consolidated and extended into the new Ruby script x3dna_ensemble:
------------------------------------------------------------------------
Utilities for the analysis and visualization of an ensemble
Usage: x3dna_ensemble [-h|-v] sub-command [-h] [options]
where sub-command must be one of:
analyze -- analyze MODEL/ENDMDL delineated ensemble (NMR or MD)
block_image -- generate a base block schematic image
extract -- extract structural parameters after running 'analyze'
reorient -- reorient models to a particular frame/orientation
------------------------------------------------------------------------
--version, -v: Print version and exit
--help, -h: Show this message
Conceivably, C programs in 3DNA can also be consolidated. For backward compatibility, however, all existing C programs will be kept — and refined as necessary — in the current 3DNA v2.x series. As of v3.x, I’ll completely re-organize 3DNA incorporating my years of experience in programming languages and knowledge of macromolecular structures.
