Hello,
I am having a little trouble with properly formatting a ligand file where Pymol is exhibiting the following error (see screenshot) for the attached pdb file. If this is something that you can simply solve please let me know, thanks if you know and have time:)
The attached file 5b1.pdb is not a pdb file. A pdb file is a plain ASCII text file, the file you attached is something quite different and of more complex structure (see screenshot for its internal structure). The error message is triggered by the fact that already the 10th character of the file cannot be interpreted under the assumption that the file is a utf-8 encoded plain-text file.
Hi Annemarie thank you so much for your kind update:).
Is there a way that I can properly convert this utf-8 encoded plain-text file to the properly formatted ASCII text file? (I generated this 3-D File from a website that converted its chemical name, 1-Benzyl-5-(dibenzylamino)-1H-indole-2-carboxylic acid, since I needed its 3D Coordinates for docking.)
Thanks if you can help further 💡
Hello Annemarie you may disregard my last inquiry, I simply used Avogadro to convert the PubChem 2-D structure to its corresponding 3-D structure.
Kind Regards,
Joel 🚀
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