These are "alternative locations", meaning that in high resolution structure, you may observe different conformations in the electron density. Depending on the programs you are using, you either need to set some parameter to tell the program to ignore all but the most highly occupied conformation, or you need to pre-process the PDB files to remove the secondary locations. Many structure visualisation programs contain options to select, and by extension, selectively delete alternative locations - check the manual for the program you are using

In VMD, you can use the PDB plugin to do so. https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/pdbplugin.html

You can also use PDBtools in Phenix https://www.phenix-online.org/documentation/reference/pdbtools.html

In Rosetta, a simple python script can be used to clean up a pdb file:

tools/protein_tools/scripts/clean_pdb.py   - Prepare PDBs for Rosetta by cleaning and renumbering residues.

https://www.rosettacommons.org/docs/latest/application_documentation/tools/Tools

in PyMOL, you can use the removal.py script: https://pymolwiki.org/index.php/Removealt or by simply specifying

remove not (alt ' '+'A')

alter all, alt=' '

These are "alternative locations", meaning that in high resolution structure, you may observe different conformations in the electron density. Depending on the programs you are using, you either need to set some parameter to tell the program to ignore all but the most highly occupied conformation, or you need to pre-process the PDB files to remove the secondary locations. Many structure visualisation programs contain options to select, and by extension, selectively delete alternative locations - check the manual for the program you are using

In VMD, you can use the PDB plugin to do so. https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/pdbplugin.html

You can also use PDBtools in Phenix https://www.phenix-online.org/documentation/reference/pdbtools.html

In Rosetta, a simple python script can be used to clean up a pdb file:

tools/protein_tools/scripts/clean_pdb.py   - Prepare PDBs for Rosetta by cleaning and renumbering residues.

https://www.rosettacommons.org/docs/latest/application_documentation/tools/Tools

in PyMOL, you can use the removal.py script: https://pymolwiki.org/index.php/Removealt or by simply specifying

remove not (alt ' '+'A')

alter all, alt=' '

Dear Dr. Annemarie Honegger ,

Really appreciate your kind answers. I followed the steps you suggest using python script in PyMol, that really solved the problem! Thank you!

Best Regards,

Faris