mkdssp(1)

🎀 mkdssp(1) 🎀

hii bestie 💖 so this is the mkdssp manual page, and it hangs out in the User Commands part of the manual — that's the (1) in mkdssp(1), iykyk. Buckle up, we're assigning secondary structure and it's gonna be iconic ✨

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🌸 NAME 🌸

mkdssp — Assign secondary structure to proteins

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✨ SYNOPSIS ✨

mkdssp [OPTION] input [output]

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🦋 DESCRIPTION 🦋

So the DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. Periodt. 💅 DSSP is a database of secondary structure assignments (and much more, lowkey) for all protein entries in the Protein Data Bank (PDB). And mkdssp is the program that calculates DSSP entries from PDB entries. Important though: mkdssp does not predict secondary structure. It's not doing fortune telling, it's doing assignment 🙈

The original DSSP program wrote output in a fixed format, but this version by default writes annotated mmCIF files, storing the secondary structure information in the _struct_conf category. Glow up fr fr ✨

And since version 4.0, the mkdssp program also assigns PPII helices. Obsessed. 🫶

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💅 OPTIONS 💅

First, the vibe check on inputs and outputs, because this part matters:

The input file can be either mmCIF or PDB format, and the file may be gzip compressed. But heads up bestie — input files must be formatted correctly. E.g. PDB files must have a CRYST1 record. More info here: https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1

The output is optional, and if you omit it the output is written to stdout. If the name of the output file ends with either .gz or .bz2 the output is compressed accordingly. Compression queen 👑

• --output-format=[dssp|mmcif] — If an output file is specified, the extension of the filename is used to choose the output format, but if it's unclear, mmcif is the default. Use this option to force output in either the old fixed column DSSP format or the new annotated mmCIF format. You're the one in charge now 💁‍♀️
• --no-dssp-categories — When writing mmCIF files, suppress the output of all dssp_ categories. Not me hiding the extra lore 🙈
• --min-pp-stretch — This option can be used to define the minimal number of residues with PHI/PSI angles within the range required to assing a PP helix. (Yes, "assing" — that's literally what the page says, no cap 😭)
• --write-other — By default the new format does not write the structure information for OTHER. Use this flag to change that. Main character energy for the loops 🌈
• --components — The knowledge of compounds is loaded from the CCD file components.cif that should have been installed by libcifpp. You can override that file by using this option. Swap it out, slay 🎀
• --extra-compounds — As an addition to the standard components.cif file, you can add more files using this option. Files should be either in CCD format or should be CCP4 restraints files. More is more, bestie ✨
• --mmcif-dictionary — The default mmCIF dictionary file is installed by the libcifpp library but you can override it using this option. Customize your dictionary, very you 💜

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🔥 DETAILS 🔥

The DSSP algorithm assings secondary structure based on the energy calculated for H-bonds. Chemistry said so 💅

Table 1. Secondary Structures recognized

• DSSP Code H → mmCIF Code HELX_RH_AL_P — Alphahelix
• DSSP Code B → mmCIF Code STRN — Betabridge
• DSSP Code E → mmCIF Code STRN — Strand
• DSSP Code G → mmCIF Code HELX_RH_3T_P — Helix_3
• DSSP Code I → mmCIF Code HELX_RH_PI_P — Helix_5
• DSSP Code P → mmCIF Code HELX_LH_PP_P — Helix_PPII
• DSSP Code T → mmCIF Code TURN_TY1_P — Turn
• DSSP Code S → mmCIF Code BEND — Bend
• DSSP Code ' ' (space) → mmCIF Code OTHER — Loop

Look at that mapping, it's giving organized 🧚

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💀 BUGS 💀

The mmCIF format currently lacks a lot of information that was available in the old format, like information about the bridge pairs or the span of the various helices recognized. Also the accessibility information is left out.

Sad but true, bestie 😭 the new format is lowkey missing receipts.

If you think this information should be part of the output, please contact the author. Speak up, we're listening 🫶

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👑 AUTHOR 👑

Written by Maarten L. Hekkelman <maarten@hekkelman.com>

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🌈 REPORTING BUGS 🌈

Report bugs at https://github.com/PDB-REDO/dssp/issues

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okay that's the whole page, you ate it 💖 this was version 4.3.2, dated 2023-06-13, and it's the mkdssp(1) page — go forth and assign some secondary structure, bestie. no cap, slay, bye ✨🎀🦋