This is my first time posting to stack exchange, as well as to using data-driven approaches, so please correct me if my questions is not clear enough.

I am trying to parse 200+ .pdb files to extract residues within 15 angstroms of a certain ligand. I have managed to extract the resnames in a text file.

In order to do a sanity check, I first ran my code on the first 5 pdb files of this list and compared the outputs to expected output. However, I was wondering if there are any other steps I can take to make my check more robust.

Are there any 'gold standard'/good practices related to this?

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    $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Jun 24, 2023 at 1:24
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    $\begingroup$ Welcome to the site. Could you kindly provide further details, e.g. are you using pymol, biopython PDB and what code have you written to date? Any reproducible example is always welcome. $\endgroup$
    – M__
    Commented Jun 24, 2023 at 2:13
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    $\begingroup$ Add a counter to be sure you're parsing the exact amount of pdbs you expect to parse ? Check for the ligand before extracting the interacting residue ? Check for duplicate pdbs ? $\endgroup$
    – pippo1980
    Commented Jun 25, 2023 at 19:31
  • $\begingroup$ Thank you @M__. I am using VMD to parse through the PDB files. I can share my algorithm as follows: 1. Load the PDB into vmd. \ 2. Identify the number of occurances of ligand, say Na+. \ 3. For each of the occurance of Na+, identify the atoms within 5A of distance from it. \ 4. Extract the resid and chain names for each of those atoms and store it as a pair in a variable pair_list. \ 5. Filter out the repeated pairs to make sure I am counting every residue only once bold**(quick Q: do you think the combo of resid and chain are sufficient to avoid repeated counting?) **bold $\endgroup$ Commented Jun 27, 2023 at 22:15
  • $\begingroup$ 6. Extract the resnames of those unique residues and save it in a text file. 7. Repeat this process for all the PDB in current directory. I have added the TCL script doing this for NH4+ at this github link: github.com/priyanshurg/TCLScripts/blob/main/… $\endgroup$ Commented Jun 27, 2023 at 22:20


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