support different file types

[Matthew Watson]

Ar e you intending to support multiple MD formats (.xtc for example) or else can you add some functionality to quickly convert between formats (the mdconvert function of MDtraj is not as user friendly as it might be), Can you also clarify the instructions for reading and or concatenating multiple ie. hundreds of PDB files from a local location, In each of these cases a worked example of the code to be entered would help enormously.

[Xinqiu Yao]

We do not have any plan in near future to support MD formats more than DCD and NetCDF. But, I believe it should be easy to convert through e.g. VMD.

If all the PDB files are the same protein (exactly the same sequence), you can concatenate them into one file out of R (using the Linux command cat, for example) and then read in as multiple models using read.pdb(…, multi=TRUE)Or, you can load them all into VMD and save as either a DCD or NetCDF file. Then, read using bio3d builtin function read.dcd() or read.ncdf()

If the files are for different proteins (e.g., homologs), the best way is to construct a pdbs object. For example,

files <- list.files('folder_of_pdb_files', '\\.pdb$', full.names=TRUE)
pdbs <- pdbaln(files)

Then, use bio3d functions to process pdbs for various calculations. Take a look of bio3d Documentations (http://thegrantlab.org/bio3d/html/index.html) or Tutorials (http://thegrantlab.org/bio3d/tutorials) for more detail.

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