Multiple Chain PDB split duplication error

[Former user]

I received the following error message using pdbsplit function of bio3d:

Warning message: In read.pdb(pdb.files[i], verbose = verbose, ...) : duplicated element numbers ('eleno') detected

It appears that PDB split will not handle a vast number of chains. I am trying to split the pdbs for a ribosome structure (PDB 4v7e). Many of the chains are named with uppercase and lower case letters which I think is creating duplicate output of pdb files. For example there is a chain "W" and a separate chain "w".

Do you know of a way to work around this issue?

[Xinqiu Yao]

Hi,

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The lower case chain ID issue was resolved long time ago. See this issue: https://bitbucket.org/Grantlab/bio3d/issues/89/pdbsplit-lower-and-upper-case

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Can you update to the latest version of bio3d and try again?

[Xinqiu Yao]

pdbsplit() can handle a large number of chains as long as chain IDs are unique (case sensitive).

However, if the number is vast, it is not recommended to use traditional PDB format any more.

In future, pdbsplit() should support other formats from PDB for large systems, such as mmCIF, PDBML/XML, or the latest MMTF. This applies to other related functions as well, e.g., get.pdb(), pdbaln(), etc.

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