read.pdb gives error in scan

[Former user]

Some times atom names might contain comma. For example, PDB: 1H5T, contain ligand DAU with atom names like "C5,". This cause an error in read.pdb with a message "Error in scan". This is because the read.pdb also use comma as delimiter. I would suggest to change the comma delimiter to something else so that these errors are avoided.

[Xinqiu Yao]

That is really a thing that we never noticed. Thanks for reporting! I noticed that there are two places related in 'read.pdb()': split.fields() and read.table(..., sep=",", ...). We may need to replace the comma with something very unlikely to appear in PDB files. What about "$"? Any other suggestion?

[Lars Skjærven]

perhaps ; (or |) ?

[Lars Skjærven]

The last bugfix in releases should work for you now. To install this version you do:

install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", ref="releases", subdir = "ver_devel/bio3d/")

> library(bio3d)
> read.pdb("1H5T")
  Note: Accessing on-line PDB file
  HEADER    TRANSFERASE                             25-MAY-01   1H5T               

 Call:  read.pdb(file = "1H5T")

   Total Models#: 1
     Total Atoms#: 9839,  XYZs#: 29517  Chains#: 4  (values: A B C D)

     Protein Atoms#: 9089  (residues/Calpha atoms#: 1160)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 750  (residues: 510)
     Non-protein/nucleic resid values: [ DAU (4), HOH (501), SO4 (1), TYD (4) ]

   Protein sequence:
      KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDT
      PRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPK
      LMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDN
      DVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLD...<cut>...MTKD

+ attr: atom, helix, sheet, seqres, xyz,
        calpha, remark, call