[phenixbb] secondary restraints

Jianghai Zhu jzhu at idi.harvard.edu
Mon Jun 21 11:55:21 PDT 2010


Hi,

I am using secondary restraints in the phenix.refine. I got the following error message.

hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'A' and resseq 160:162) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'A' and resseq 160:162) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'A' and resseq 242:244) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'A' and resseq 242:244) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'A' and resseq 360:363) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'A' and resseq 360:363) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'A' and resseq 387:389) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'A' and resseq 387:389) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'A' and resseq 455:457) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'A' and resseq 455:457) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 143:152) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 143:152) and (altloc 'A' or altloc ' ') and name O" => 10 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 156:165) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 156:165) and (altloc 'A' or altloc ' ') and name O" => 10 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 190:193) and (altloc 'A' or altloc ' ') and name H" => 1 donors
  "(chain 'B' and resseq 190:193) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 222:227) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 222:227) and (altloc 'A' or altloc ' ') and name O" => 6 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 243:251) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 243:251) and (altloc 'A' or altloc ' ') and name O" => 9 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 253:256) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 253:256) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 278:282) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 278:282) and (altloc 'A' or altloc ' ') and name O" => 5 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 301:305) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 301:305) and (altloc 'A' or altloc ' ') and name O" => 5 acceptors
hydrogen_bonds_from_selections: incomplete non-PRO residues in helix.
  "(chain 'B' and resseq 311:321) and (altloc 'A' or altloc ' ') and name H" => 0 donors
  "(chain 'B' and resseq 311:321) and (altloc 'A' or altloc ' ') and name O" => 11 acceptors
Traceback (most recent call last):
  File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/command_line/refine.py", line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/refinement/command_line.py", line 71, in run
    overwrite = command_line_interpreter.command_line.options.overwrite)
  File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/refinement/driver.py", line 121, in __init__
    h_bond_table = self.sec_str.get_bonds_table(log=log)
  File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 1023, in get_bonds_table
    log=log)
  File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 444, in hydrogen_bonds_from_selections
    ss_type="helix")
  File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 652, in _donors_and_acceptors
    donor_isel.insert(k, n_atoms)
IndexError: Index out of range.


How do I fix it?  Thanks.

-- Jianghai







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