Fetching PDB files from RCSB

[josef0731]

@jkleinj I found out there are PDB entries which violate the current R code for fetching coordinates from the RCSB server - 6zlr is one of those - the following is the shiny-server log when I put this accession ID into the text box and clicked 'run POPSCOMP' (whereas towards the end you will see I tried with another entry 5mov which the server successfully fetched PDB file):

trying URL 'https://files.rcsb.org/download/6zlr.pdb'
Warning in download.file(get.files[k], put.files[k], quiet = !verbose) :
  cannot open URL 'https://files.rcsb.org/download/6zlr.pdb': HTTP status was '404 Not Found'
Warning in file.remove(put.files[k]) :
  cannot remove file '/tmp/POPScomp_a5db54a637aeac0fcb3717d4e867e643/6zlr.pdb', reason 'No such file or directory'
Warning in get.pdb(input$pdbentry, path = outDir) :
  Some files could not be downloaded, check returned value
Warning: Error in pdbsplit: No corresponding PDB files found
  127: stop
  126: pdbsplit
  125: popscompR
  124: eventReactiveValueFunc [/srv/shiny-server/POPSCOMP/app.R#405]
   80: output$nil
    1: runApp
trying URL 'https://files.rcsb.org/download/5mov.pdb'
downloaded 264 KB

I then had a look at https://www.rcsb.org/downloads? and it seems 6zlr does not have a .ent or .pdb file - it has coordinates in cif format, and cif files for individual assemblies.

If one looks at PDBe the same entry also does not have a PDB format file available for download - but there is something called Compatible PDB file bundle (tar.gz). I wonder if this is to do with PDB slowly moving away from PDB format and making cif as the standard? The POPSCOMP code probably needs to deal with this (or try for this 'PDB file bundle' and extract the coordinates from therein if the default RCSB download link returns an error?)