Processed Receptor has Long Legs in PDB File

[syedzayyan]

Hello!

I am trying PDBFixer to clean up a PDB file (6D9H) and when I remove the complexed proteins from the receptor, the resulting receptor file is left with long bits (that I am calling legs) sticking out. I tried OpenMM Setup as well. This is the file from openmm-setup.

7ld4-processed.pdb.zip

Any idea how to fix this issue?

This is the code, which is very similar to openmm-setup that I am trying:

chains_to_delete = []
hasHeterogen = False
for chain in fixer.topology.chains():
    if chain.id != 'R':
        chains_to_delete.append(chain.index)
fixer.removeChains(chainIndices=chains_to_delete)

fixer.addMissingAtoms()
fixer.addMissingHydrogens(7.0)
fixer.removeHeterogens()

[peastman]

Many proteins have flexible tails at the ends. Because they're flexible, they generally can't be resolved by crystallography, so they're missing from crystal structures. PDBFixer adds them sticking outward in a straight line, just because that's an easy way to do it, but don't think it means anything. The whole point is that they're flexible. They don't have a fixed conformation.

In some proteins the tails are functionally important. In others they can be safely removed, and it won't affect the function of the protein.

[syedzayyan]

That's what I guessed. For a hassle-free clean separation of pdb file into chains, I found this tool by Bonvin Lab called pdb-tools, in case someone runs into the issue again.

Thank you for the comments and help!

[groponp]

Dear in case that i don't like c and n terminal residues, there is any example?

Using example from you docs, say me missingResidues.keys not exist

[peastman]

The manual gives an example of adding residues only in the middle of chains but not at the ends.

fixer.findMissingResidues()
chains = list(fixer.topology.chains())
keys = fixer.missingResidues.keys()
for key in keys:
    chain = chains[key[0]]
    if key[1] == 0 or key[1] == len(list(chain.residues())):
        del fixer.missingResidues[key]
fixer.findNonstandardResidues()

[groponp]

It is my code: PDB used 5x00

    def missing(self, ifile, keep_chain="all"): 
        #self.download_pdb(PDBcode)
        PDBname = ifile
        IO().message("Adding missing atoms to the file {}".format(PDBname), tm="INFO")
        fixer = PDBFixer(filename=PDBname)
        fixer.findMissingResidues()
        chains = list(fixer.topology.chains())
        keys = fixer.missingResidues.keys()
        for key in keys:
            chain = chains[key[0]]
            if key[1] == 0 or key[1] == len(list(chain.residues())):
                del fixer.missingResidues[key]
        fixer.findNonstandardResidues()
        fixer.replaceNonstandardResidues()
        fixer.removeHeterogens(True)
        fixer.findMissingAtoms()
        fixer.addMissingAtoms()]

and ERROR IS:

File "/Volumes/Galvani/Scripts/easyHTMD/test/../easyHTBMD.py", line 73, in fixername = PDB().missing(ifile=filename, keep_chain="all") File "/Volumes/Galvani/Scripts/easyHTMD/src/PDB.py", line 84, in missing for key in keys: RuntimeError: dictionary changed size during iteration

[peastman]

Try changing it to

keys = list(fixer.missingResidues.keys())

[groponp]

Thanks it help so much. A more question as evite add N an C terminal?, only using it is suitable?

[peastman]

Sorry, I don't understand your question?

[groponp]

"I would like to know, on the one hand, if using this code, it is safe to prevent the N- and C-terminal regions from being added, for example: if one has a protein of 100 amino acids and only the region from 50 to 90 was resolved by X-ray, does this code prevent residues from 1 to 59 and from 91 to 100 from being added? On the other hand, I would like to know what is the output nomenclature of the PDB. Amber ff, CHARMM ff?

[peastman]

Correct. The terminal regions will not be added.

It uses standard PDB nomenclature, as specified in the PDB Chemical Components Dictionary. The output should fully comply with the PDB spec.

[groponp]

Dear when using fixer.addMissingHydrogens(7.0), as i can specify charmm ff nomenclature for output?

[peastman]

No, it always produces standard PDB files. CHARMM has a format that it calls "PDB", but it isn't really. It's a proprietary format used only by CHARMM. It differs from the real PDB format in several ways.

[groponp]

Is this method correct for assigning protonation states to residues? For example, I am using NAMD to read the fixed PDB, so when it reads the PDB with psfgen, could it differentiate, for instance, between HIP (+1 charged, both δ- and ε-nitrogens protonated), HID (neutral, δ-nitrogen protonated), and HIE (neutral, ε-nitrogen protonated)? So that I can obtain this in the final result? Or do I have to do this manually? Because when using PDB2PQR, it generates incorrect results.

[peastman]

You're asking questions that are unrelated to this issue. Could you open a new issue instead of tacking them on to this one? Thanks!