Why is my PDB file not opening correctly in PyMol (version 2.5.4)?

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Nikolaos Kourkoumelis

Open the pdb with a different software (e.g., chimera https://www.cgl.ucsf.edu/chimera/) and check it. If it seems to be ok, export it from chimera to a new pdb and re-open it to pymol.

Satyendra Singh

There could be several reasons why your PDB file is not opening correctly in PyMol. Here are a few potential solutions to try:

Check the PyMol version: Make sure that the version of PyMol that you are using is compatible with your PDB file. It's possible that your PDB file was created using a newer version of PyMol that is not compatible with your current version. Try updating your PyMol version and see if that resolves the issue.

Check the file format: Double-check that your PDB file is in the correct format. PyMol may have difficulty opening files that are not in the proper PDB format. You can try opening the file in a text editor and ensuring that it is formatted correctly.

Try a different viewer: If your PDB file is not opening correctly in PyMol, try opening it in a different molecular visualization software, such as Chimera or VMD. If the file opens correctly in another viewer, it may indicate a problem with your PyMol installation.

Check for missing atoms: It's possible that there are missing atoms or other errors in your PDB file. Try running the PDB file through a validation tool, such as MolProbity, to check for any structural issues.

Try adjusting display settings: If the issue is related to how the PDB file is being displayed in PyMol, try adjusting the display settings. For example, you can try changing the display style or adjusting the zoom level to see if that resolves the issue.

If none of these solutions work, you may want to seek further assistance from the PyMol support team or an expert in structural biology.

Lorenzo Briganti

I would say probably either missing atoms, or wrong chain IDs. Make sure you have everything properly, you can check with GEDIT or any other text software.