- edited description
1JTW error
Hi! I recently discovered that the PDB 1JTW gives an error when I try to read multiple models:
library(bio3d); pdb <- read.cif("1JTW", multi=T)
Note: Accessing on-line CIF file
Warning messages: 1: In read.cif("1JTW", multi = T) : helix/sheet records will not be parsed in this version of the code
2: In get.pdb(file, path = tempdir(), quiet = TRUE, format = "cif") : /tmp/Rtmp6NsTxE/1JTW.cif exists. Skipping download
3: In matrix(pdb$xyz, nrow = pdb$models, byrow = TRUE) : data length [22536] is not a sub-multiple or multiple of the number of rows [14]
4: In as.xyz(pdb$xyz) : number of cartesian coordinates not a multiple of 3
I though it was worth sharing with you! Cheers,
Diego
Comments (6)
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reporter -
reporter - edited description
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Thanks for reporting Diego. There are unequal number of atoms between the different models in the PDB file. i.e 537, 538, 539 and 524 atoms.
The previous version of read.pdb , (found in function read.pdb2()) provides a cleaner error message:
> pdb = read.pdb2("1jtw.pdb", multi=T) PDB has multiple END/ENDMDL records multi=TRUE: 'read.dcd/read.ncdf' will be quicker! HEADER RNA 22-AUG-01 1JTW Warning message: In read.pdb2("1jtw.pdb", multi = T) : Unequal number of atoms in multi-model records: 1jtw.pdb
Todo:
- cleaner error messages for read.cif and new read.pdb
- explore ways to account for the different number of atoms
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assigned issue to
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assigned issue to
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- changed component to ToDo
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- marked as proposal
Not a bug but because of bad format of input files.
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