pymol.CmdException: Error: Object not found

[Le-Phung-Hien]

The program was run on Windows 11 with Anaconda as the Python packet manager.

I have installed all necessary package via Anaconda (conda install -c conda-forge plip) and have the PLIP source code folder. Also created an alias (doskey="python plipcmd.py"). While running PLIP to analyse a local pdb file with the command (plip -f "file path" -v -y -p), the program cannot generate PyMOL session files and PyMOL Ray-traced images.

This is the full text appeared:
plip -f D:\5555555.pdb -v -y -p 2022-09-22 11:30:47,211 [INFO] [plipcmd.py:124] plip.plipcmd: Protein-Ligand Interaction Profiler (PLIP) 2.2.2 2022-09-22 11:30:47,211 [INFO] [plipcmd.py:125] plip.plipcmd: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - [email protected] 2022-09-22 11:30:47,211 [INFO] [plipcmd.py:126] 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 2022-09-22 11:30:47,211 [INFO] [plipcmd.py:49] plip.plipcmd: starting analysis of D:\5555555.pdb Warning: Invalid characters in 'D_5555555_Protein' have been replaced or stripped Traceback (most recent call last): File "C:\Users\lephu\.conda\envs\plip\Scripts\plip-script.py", line 9, in <module> sys.exit(main()) File "C:\Users\lephu\.conda\envs\plip\lib\site-packages\plip\plipcmd.py", line 309, in main run_analysis(expanded_path, arguments.pdbid) # Start main script File "C:\Users\lephu\.conda\envs\plip\lib\site-packages\plip\plipcmd.py", line 150, in run_analysis process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin, outputprefix=output_prefix) File "C:\Users\lephu\.conda\envs\plip\lib\site-packages\plip\plipcmd.py", line 77, in process_pdb [visualize_in_pymol(plcomplex) for plcomplex in complexes] File "C:\Users\lephu\.conda\envs\plip\lib\site-packages\plip\plipcmd.py", line 77, in <listcomp> [visualize_in_pymol(plcomplex) for plcomplex in complexes] File "C:\Users\lephu\.conda\envs\plip\lib\site-packages\plip\visualization\visualize.py", line 86, in visualize_in_pymol vis.refinements() File "C:\Users\lephu\.conda\envs\plip\lib\site-packages\plip\visualization\pymol.py", line 435, in refinements cmd.copy('%sCartoon' % self.protname, self.protname) File "C:\Users\lephu\.conda\envs\plip\lib\site-packages\pymol\creating.py", line 889, in copy r = _cmd.copy(_self._COb,str(source),str(target),int(zoom)) pymol.CmdException: Error: Object not found.

The output is a protonated file.

Thank you very much!