-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello. 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 prefixableType=1) 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 - -- 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@cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées

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