DOMAINRESO(1e)

📦 version 0.1.660, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 DOMAINRESO 💖

okay bestie, welcome to domainreso from the EMBOSS Manual for Debian — yes, that 1e up in the corner means it's an EMBOSS tool, and yes, it's giving very "niche science girlie" energy but we're obsessed anyway ✨

🌸 NAME 🌸

domainreso — the way that this literally just removes low resolution domains from a DCF file. that's it. that's the whole vibe. periodt 💅

✨ SYNOPSIS ✨

domainreso -cpdbpath dirlist -dcfinfile infile -threshold float
           -dcfoutfile outfile

domainreso -help

🦋 DESCRIPTION 🦋

so domainreso is a command line program from EMBOSS, aka "the European Molecular Biology Open Software Suite" 🌈. it's part of the "PROTEIN:3D STRUCTURE" command group(s), so if you're into protein 3D structure stuff, this is your girl 🫶

🎀 OPTIONS 🎀

🌟 Input section 🌟

  • -cpdbpath dirlist — this one tells the program where to find the domain CCF files (clean coordinate files) — that's an input, bestie. and ngl, a 'clean cordinate file' is literally the cutest concept: it contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, all in CCF format (EMBL-like). these files get generated by using PDBPARSE (for pdb files) or DOMAINER (for domains), and they contain 'cleaned-up' data that is self-consistent and error-corrected 😌✨. records for residue solvent accessibility and secondary structure get added to the file by using PDBPLUS. Default value: ./
  • -dcfinfile infile — this specifies the name of the DCF file (domain classification file) — also an input. a 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). these files are generated by using SCOPPARSE and CATHPARSE. and domain sequence information can be added to the file by using DOMAINSEQS 👑

💅 Required section 💅

  • -threshold float — this sets the threshold for inclusion, in Angstroms. heads up though: domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file 🫢. so it's a "you must be this resolved to ride" situation fr fr. Default value: 2.8

🍓 Output section 🍓

  • -dcfoutfile outfile — the name of the DCF file (domain classification file) on the way out this time. same deal as before: a 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like), generated by using SCOPPARSE and CATHPARSE, and domain sequence information can be added by using DOMAINSEQS 🌸. Default value: test.scop

😭 BUGS 😭

found a bug? not me being the bearer of bad news but — bugs can be reported to the Debian Bug Tracking system at http://bugs.debian.org/emboss, or you can go straight to the EMBOSS developers at http://sourceforge.net/tracker/?group_id=93650&atid=605031 🐛

👀 SEE ALSO 👀

domainreso is fully documented via the tfm(1) system. iykyk 💜

🫶 AUTHOR 🫶

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page. iconic honestly 👑

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. so like, share responsibly bestie 💖

and that's the whole thing!! this lil page is part of DOMAINATRIX 0.1.0+20100721, dated 08/11/2010 — ancient but still slaying, no cap ✨🎀🦋💅

📦 where this page comes from