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jaimergp / prep-mcpb

Prepare a metal-containing structure for parameterization with MCPB.py using UCSF Chimera and AmberTools
MIT License
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non-protein files #5

Closed sara-netbeans closed 4 years ago

sara-netbeans commented 4 years ago

Hello,

Could you please briefly describe the procedure to process non-protein files (or an example).

I have installed the program on my MacOS station and it works well with the example files 1OKL and 4ZF6.

For my structure cage I get the follow message error :

Opening pdb:test Traceback (most recent call last): File "prep-mcpb.py", line 537, in args = main() File "prep-mcpb.py", line 509, in main charge_method=args.chargemethod) File "prep-mcpb.py", line 58, in prepare_molecule_files structure = load_structure(structure_query, strip=strip) File "prep-mcpb.py", line 103, in load_structure chimera.runCommand('open ' + query) File "/Applications/Chimera.app/Contents/Resources/share/chimera/init.py", line 2791, in runCommand makeCommand(*args, *kw) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 1616, in doOpen modelArg, noprefs) File "", line 1, in File "/Applications/Chimera.app/Contents/Resources/share/Midas/init.py", line 2212, in open noprefs=noprefs) File "/Applications/Chimera.app/Contents/Resources/share/chimera/init.py", line 1955, in open models = func(filename, args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/init.py", line 1082, in _openPDBModel return _openPDBIDModel(filename) File "/Applications/Chimera.app/Contents/Resources/share/chimera/init.py", line 860, in _openPDBIDModel ignore_cache=ignore_cache) File "/Applications/Chimera.app/Contents/Resources/share/chimera/init.py", line 911, in _openCIFIDModel 'PDB', '%s.cif' % IDcode.upper(), ignore_cache=ignore_cache) File "/Applications/Chimera.app/Contents/Resources/share/chimera/init.py", line 807, in _pdbFetch raise UserError, "No such ID: %s" % statusName chimera.UserError: No such ID: test

Best regards,