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Residue number strange behavior #201
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This problem is intrinsic to the PDB format. It only gives four columns for the residue ID, which means a strictly compliant PDB file can never have more than 10,000 residues. It also only gives five columns for the atom ID, so you're limited to 100,000 atoms, and one column for the chain ID, which limits you to 26 chains (since chain IDs are supposed to be upper case letters). Of course, people frequently try to write larger systems to PDB files, so a variety of non-compliant hacks get used to deal with that. Wrapping the IDs back to 0 is one of the more common ones. The real solution, though, is to write to a PDBx/mmCIF file instead. It's the successor to the PDB format, and it fixes these problems and many others. Just change |
I see, but as said, even if I didn't put it in the example, the exact same thing happens when using the mmCIF/PDBx file. This means that the problem is format independent. This problem happened only with this specific protein, so I guess that it might be a "patological" situation but it could reveal some kind of sneaky bug. Here is the .cif file with the exact same problem: Thank you very much for your time and have a nice day. |
Hello,
I found a strange behavior when repairing the 6w02 from the wwPDB (this happens both for the PDB and mmCIF file, the example below is for the PDB file):
When i repair the 6w02 protein the first lines of the repaired PDB look like this:
As you can see the first residue starts from number 9998 an then this brings in having a residue 0 (zero), and this happens for both chain A and B. And as the original PDB starts from residue 4 it doesn't make much sense.
And having this 2 residue 0 (chain A and chain B) gives big problems when dealing with the protein structures with tools like Biopython
both the input and output files are attached as .txt files
Thank you very much and have a nice day
output6w02.txt
pdb6w02.txt
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