---
name: "plipcmd"
section: "1"
platform: "linux"
package: "plip"
version: "2.4.0+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/plipcmd"
---

# plipcmd(1)

Protein-Ligand Interaction Profiler (PLIP)

## NAME

plipcmd - Protein-Ligand Interaction Profiler (PLIP)

## DESCRIPTION

usage: PLIP \[-h\] (**-f** INPUT \[INPUT ...\] \| **-i** PDBID \[PDBID ...\]) \[-o OUTPATH \|

-

  **-O\]** \[--rawstring\] \[-v\] \[-q\] \[-s\] \[-p\] \[-x\] \[-t\] \[-y\] \[--maxthreads MAXTHREADS\] \[--breakcomposite\] \[--altlocation\] \[--nofix\] \[--nofixfile\] \[--nopdbcanmap\] \[--dnareceptor\] \[--name OUTPUTFILENAME\] \[--peptides PEPTIDES \[PEPTIDES ...\] \| **--intra** INTRA\] \[--residues RESIDUES \[RESIDUES ...\]\] \[--keepmod\] \[--nohydro\] \[--model MODEL\] \[--chains CHAINS\]

The Protein-Ligand Interaction Profiler (PLIP) Version 2.4.0 is a command-line based tool to analyze interactions in a protein-ligand complex. If you are using PLIP in your work, please cite: Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294 Supported and maintained by: PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai

### options:

- **-h**, **--help**

  show this help message and exit

- **-f**, **--file** INPUT \[INPUT ...\]

  Set input file, '-' reads from stdin

**-i**, **--input** PDBID \[PDBID ...\]

**-o**, **--out** OUTPATH

- **-O**, **--stdout**

  Write to stdout instead of file

- **--rawstring**

  Use Python raw strings for stdin

- **-v**, **--verbose**

  Turn on verbose mode

- **-q**, **--quiet**

  Turn on quiet mode

- **-s**, **--silent**

  Turn on silent mode

- **-p**, **--pics**

  Additional pictures

- **-x**, **--xml**

  Generate report file in XML format

- **-t**, **--txt**

  Generate report file in TXT (RST) format

- **-y**, **--pymol**

  Additional PyMOL session files

- **--maxthreads** MAXTHREADS

  Set maximum number of main threads (number of binding sites processed simultaneously).If not set, PLIP uses all available CPUs if possible.

- **--breakcomposite**

  Don't combine ligand fragments with covalent bonds but treat them as single ligands for the analysis.

- **--altlocation**

  Also consider alternate locations for atoms (e.g. alternate conformations).

- **--nofix**

  Turns off fixing of PDB files.

- **--nofixfile**

  Turns off writing files for fixed PDB files.

- **--nopdbcanmap**

  Turns off calculation of mapping between canonical and PDB atom order for ligands.

- **--dnareceptor**

  Treat nucleic acids as part of the receptor structure (together with any present protein) instead of as a ligand.

- **--name** OUTPUTFILENAME

  Set a filename for the report TXT and XML files. Will only work when processing single structures.

- **--peptides**, **--inter** PEPTIDES \[PEPTIDES ...\]

  Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts

- **--intra** INTRA

  Allows to define one chain to analyze intra-chain contacts.

- **--residues** RESIDUES \[RESIDUES ...\]

  Allows to specify which residues of the chain(s) should be considered as peptide ligands. Give single residues (separated with comma) or ranges (with dash) or both, for several chains separate selections with one space

- **--keepmod**

  Keep modified residues as ligands

- **--nohydro**

  Do not add polar hydrogens in case your structure already contains hydrogens.

- **--model** MODEL

  Model number to be used for multi-model structures.

- **--chains** CHAINS

  Specify chains as receptor/ligand groups, e.g., '\[\['A'\], \['B'\]\]'. Use format \[\['A'\], \['B', 'C'\]\] to define A as receptor, and B, C as ligands.