[bug #14428] palmer.py problem wihen spins have no data -- October 02, 2009 - 20:04

URL:
  <http://gna.org/bugs/?14428>

                 Summary: palmer.py problem wihen spins have no data
                 Project: relax
            Submitted by: None
            Submitted on: Friday 10/02/2009 at 20:04 CEST
                Category: relax's source code
                Severity: 4 - Important
                Priority: 5 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: None
         Originator Name: 
        Originator Email: pierre-yves.savard@xxxxxxxxxxxxx
             Open/Closed: Open
         Discussion Lock: Any
                 Release: Repository: 1.3 line
        Operating System: GNU/Linux

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Details:

Hi,

I think I found a bug in the palmer.py script. When running stage 2, the
program stops (with error) when it tries to extract m3 (relax>
palmer.extract(dir='m3')). The problem happens if the sequence file contains
residues for which there are no data. It works fine if the sequence file
contains only residues with data.

Here is the error message:

Traceback (most recent call last):
  File "/usr/local/packages/relax-1.3/relax", line 420, in <module>
    Relax()
  File "/usr/local/packages/relax-1.3/relax", line 128, in __init__
    self.interpreter.run(self.script_file)
  File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 276, in
run
    return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
  File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 545, in
run_script
    return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 441, in
interact_script
    exec(compile(open(script_file).read(), script_file, 'exec'), local)
  File "palmer-stage2.py", line 154, in <module>
    exec_stage_2(pipes)
  File "palmer-stage2.py", line 104, in exec_stage_2
    palmer.extract(dir=name)
  File "/usr/local/packages/relax-1.3/prompt/palmer.py", line 198, in
extract
    palmer.extract(dir=dir)
  File "/usr/local/packages/relax-1.3/generic_fns/palmer.py", line 692, in
extract
    spin.rex = spin.rex / (2.0 * pi * spin.frq[0])**2
IndexError: list index out of range


Thank you,

Pierre-Yves




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