[phenixbb] quick clashlist or molprobity in batch mode

jan jan.abendroth at gmail.com
Wed Mar 6 15:36:10 PST 2013

Hi all,
I want to analyze a whole bunch of structures with molprobity, and I am looking for a convenient way to do this.

phenix.quick_clashlist seems to be a handy tool. However, when I use the following command line:
 "phenix.quick_clashlist model=mypdb.pdb"
... the output tells me:
#                       run_clashlist
# Run reduce and molprobity 
# type phenix.run_clashlist: --help for help
Parameters used:
run_clashlist {
  model = "4iuj.pdb"
  build = True
  summary_file = None
  output_file = None
  temp_dir = None
  remove_temp_dir = None
  verbose = False
  raise_sorry = False
  debug = False
  dry_run = True

'str' object has no attribute '_anchor'

Any ideas what I need to do differently?

Jan Abendroth
Emerald BioStructures
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com

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