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zrqiao / NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
https://doi.org/10.1038/s42256-024-00792-z
BSD 3-Clause Clear License
260 stars 68 forks source link

How to open results? #51

Open GXcells opened 3 months ago

GXcells commented 3 months ago

Hi, thanks a lot for NeuralPlexer.

Unfortunately, I cannot open the sdf output files in ChimeraX. I get error

IndexError: list index out of range File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\sdf\sdf.py", line 276, in read_data_line atoms[index].charge = charge See log for complete Python traceback.

is there another way to read the pdb + sdf complex files?

autodataming commented 2 months ago

Hi, thanks a lot for NeuralPlexer.

Unfortunately, I cannot open the sdf output files in ChimeraX. I get error

IndexError: list index out of range File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\sdf\sdf.py", line 276, in read_data_line atoms[index].charge = charge See log for complete Python traceback.

is there another way to read the pdb + sdf complex files?

you can try the software PyMOL

GXcells commented 2 months ago

Thanks a lot but Pymol is not free.

punit-jha123 commented 2 months ago

pymol has a free version -- https://www.blopig.com/blog/2022/03/how-to-install-open-source-pymol-on-windows-10/

GXcells commented 2 months ago

pymol has a free version -- https://www.blopig.com/blog/2022/03/how-to-install-open-source-pymol-on-windows-10/

Thanks a lot it worked