[Chimera-users] Selection question in --nogui mode

Miguel Ortiz Lombardia miguel.ortiz at cnio.es
Thu May 26 08:17:26 PDT 2005

Hash: SHA1


I'm trying to execute this:

$chimera --nogui cmd:findselhbonds

where the file findselhbonds contains:

open 01.pdb
select :59-62
hbonds selRestrict any saveFile tmp.bonds

In the graphic mode those instructions work as expected, however in the
- --nogui mode I get this error:

Opening 01.pdb...
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
Computed secondary structure assignments (see reply log)
Model 0 (01.pdb) appears to be a protein with no
secondary structure assignments.  Computing assignments
for it using the ksdssp algorithm (Kabsch and Sander Define
Secondary Structure of Proteins) with an energy cutoff of
- -0.5, minimum helix length of 5, and minimum strand length
of 4.  If these parameters don't produce good results for
this structure, you can rerun the algorithm with different
settings using the 'compute SS' button in the model panel
(under 'infrequent' actions) or via the 'ksdssp' command in
the Midas emulator.  The model panel will also allow you to
save new default parameters.
1 model opened
Opened 01.pdb containing 1 model, 632 atoms, and 62 residues
Error while processing cmd:forchimera:
NameError: global name 'selMode' is not defined
(see reply log for Python traceback info)
Traceback (most recent call last):
  File "/usr/local/linux_prg/Chimera/share/__main__.py", line 59, in ?
    value = chimeraInit.init(sys.argv)
  File "CHIMERA/share/chimeraInit.py", line 287, in init
  File "CHIMERA/share/chimera/__init__.py", line 1043, in open
  File "CHIMERA/share/Midas/ChimeraExtension.py", line 17, in func
  File "CHIMERA/share/Midas/midas_text.py", line 88, in processCommandFile
  File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand
  File "CHIMERA/share/Midas/midas_text.py", line 1039, in doSelect
  File "CHIMERA/share/Midas/__init__.py", line 620, in chimeraSelect
  File "CHIMERA/share/chimera/tkgui.py", line 1604, in selectionOperation
NameError: global name 'selMode' is not defined

Any clues?
Thank you very much!

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: miguel.ortiz at cnio.es
- -----------------------------------------------------------------------
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