When outputting the result files, only two PBD files were produced, without the result files report.txt, report.xml, and pymol.pse.

[25liuzuyan]

I used the web version of PLIP, and it produced results correctly when I input my PBD format file.
The results are the same when I use the standard test pbd format file.
(plip_new) [chenjy@prosrpsite lzy]$ plip -f 1A0Q.pdb -o test_output -v None 2025-05-28 09:52:44,163 [INFO] [plipcmd.py:134] plip.plipcmd: Protein-Ligand Interaction Profiler (PLIP) 2.4.0 2025-05-28 09:52:44,163 [INFO] [plipcmd.py:135] plip.plipcmd: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai 2025-05-28 09:52:44,163 [INFO] [plipcmd.py:136] plip.plipcmd: 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 2025-05-28 09:52:44,163 [INFO] [plipcmd.py:60] plip.plipcmd: starting analysis of 1A0Q.pdb 2025-05-28 09:52:44,977 [INFO] [plipcmd.py:175] plip.plipcmd: finished analysis, find the result files in test_output/
The environment configuration is normal.
`(plip_new) [chenjy@prosrpsite lzy]$ obabel --version
No input file or format spec or possibly a misplaced option.
Most options must come after the input files. (-i -o -O -m can be anywhwere.)

Open Babel 3.1.0 -- Nov 30 2023 -- 20:41:16
Usage:
obabel [-i] [-o] -O [Options]
Try -H option for more information.
(plip_new) [chenjy@prosrpsite lzy]$ pymol --version
PyMOL 3.0.0 Open-Source (c7e389c0f6), 2024-05-28
(plip_new) [chenjy@prosrpsite lzy]$ ^C
(plip_new) [chenjy@prosrpsite lzy]$ plip --version
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]
PLIP: error: one of the arguments -f/--file -i/--input is required
`
What is the reason for this?

[PhiCMS]

Hey,

the issue is with the command you are using (plip -f 1A0Q.pdb -o test_output -v). The output flag -o only sets the output path but does not define what kind of output should be produced. You can add -p (Pictures), -x (XML), -t (txt), -y (pymol).

E.g. to add everything you can just use:

plip -f 1A0Q.pdb -xpty -o test_output -v

Keep in mind that the picture and pymol options do require a running pymol version.

Cheers,

Philipp