Problem reading multiframe PDB with read.pdb()

Hi,

I have a problem loading multiframe/model PDB file prepared in VMD from MD trajectory in an updated version of Bio3D - 2.3-3. My concern is that everything was working fine in version 2.2-3 and it would be very helpful for me to have it working again.

The problem is that even though the structure is loaded with multi=TRUE, it is not correctly split into models / frames. Instead, it is taken as a one huge molecule I assume. There is a warning message when files is loaded.

pdb <- read.pdb("TestPDB.pdb", multi=TRUE)
Warning message:
In read.pdb("TestPDB.pdb ",  :
  duplicated element numbers ('eleno') detected

Accessing the pdb object after loading gives:

Call:  read.pdb(file = "TestPDB.pdb",   multi = TRUE)

   Total Models#: 1
     Total Atoms#: 259600,  XYZs#: 778800  Chains#: 1  (values: X)

     Protein Atoms#: 224000  (residues/Calpha atoms#: 12800)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

....

Frames / models are split only with “END” lines in a PDB file, perhaps that is the reason.

Thank you in advance, Michal

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