Troubleshooting Residue Visualization Beyond 112 in PyMOL (PDB ID: 7K3N)

[Tahir HB]

Hi everyone,

I’m working with the SARS-CoV-2 spike protein structure (PDB ID: 7K3N ) using PyMOL. I’m trying to visualize specific residues, but I’ve encountered an issue where I can’t go beyond residue 112. Details of the Issue:

• Structure: The PDB file for 7K3N is loaded successfully in PyMOL.
• Commands Used:
  • select resi 112: Successfully selects residue 112.
  • select resi 113 or higher: Fails to select any residues beyond 112.
• Error Message: No explicit error message appears, but the selection command returns no atoms for residues beyond 112.
• Sequence Check: Using iterate all, print(resi) confirms that residue numbering exists up to at least residue 1000, but visualization stops at 112.

What I’ve Tried:

1. Loaded the structure using fetch 7K3N.
2. Attempted selecting residues using both resi and chain A/resi syntax.
3. Visual inspection using commands like show sticks, resi 110-114 to verify nearby residues, but residues beyond 112 are not visible.

Questions:

1. Could this be due to missing data in the PDB file beyond residue 112?
2. Are there known issues with residue numbering or chain identifiers in this structure?
3. Are there alternative tools or methods I can use to ensure complete visualization of the structure?

[Tahir HB]

Thanks for the sturectured response. I checked & rechecked several times fasta it also reversed ordered it as well, the data on the residue is incomplete, i was looking for potential research areas in this and i found a one, resude after 112 are least studied, i think thats the potential area where intensive research can be done and it will improve drugs targetting. TMPRSS & ACE2 response will improve. But i am very disapponted to say that i will not be able to do a sequence on this or add any further reporting of the residues beyond 112 because of the lack of any research facility. I am from pakistan and we have such corrupt people there that they will always beg other countries to give research patent products but will never use their minds in good practices. anyways, now i will explore other resarch areas and will put out results of my theoretical study. Thanks by the way for help!