PDB SPLIT ISSUE

[Former user]

Hi, i am trying to split the chain to chains, all 44 pdbs are downloaded, except the one modelled, as i run the script getting following issue:

ids <- c (pdbs) raw.files <- get.pdb(ids) There were 45 warnings (use warnings() to see them) warnings are like that(In get.pdb(ids) : ./.pdb exists. Skipping download files <- pdbsplit(raw.files, ids)

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| | 0% |
|== | 2%Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines, : basic_string::substr: __pos (which is 30) > this->size() (which is 14)

Help in this regards, Thanks

[Xinqiu Yao]

Hi,

‌

It is possible that some PDB file(s) are broken. Can you check which files caused the error? You can turn on verbose=TRUE in pdbsplit(), which may help you identify the files.

[Qazi Muhammad Usman]

Hi, Thanks for your answer, but it didn’t worked for me, agan:
files <- pdbsplit(raw.files,verbose=TRUE)

.. 3249 atom(s) from 'chain' selection
.. 3249 atom(s) in final combined selection

Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines, :
basic_string::substr: __pos (which is 30) > this->size() (which is 14)

‌

[Xinqiu Yao]

What I meant is by verbose=TRUE it will print some similar messages (such as XXXX atom(s) from ‘chain’ selection) for every PDB file it processed. By counting the number of unique such message before it stops, you can infer what PDB caused the problem. Then, you need to look into that PDB file and see if anything is wrong.