<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" size="4">Hi Nat,</font><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4"><br></font><div><div><font class="Apple-style-span" size="4">On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:</font></div><blockquote type="cite"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div style=""><font class="Apple-style-span" size="4">The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py? </font></div></div></div></div></blockquote><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">Yes, that is the script I'm running.</font></div><div><font class="Apple-style-span" size="4"><br></font></div><font class="Apple-style-span" size="4"><br></font><blockquote type="cite"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div style=""><font class="Apple-style-span" size="4">Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback.</font></div></div></div></div></blockquote><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">Here's the results:</font></div><div><font class="Apple-style-span" size="4"><br></font></div></div></div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div><div><div><font class="Apple-style-span" face="Monaco">% setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1</font></div><div><font class="Apple-style-span" face="Monaco">% cctbx.python ./tst_sa.py</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco">Traceback (most recent call last):</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "./tst_sa.py", line 267, in <module></font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> exercise_1()</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "./tst_sa.py", line 122, in exercise_1</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> pi = get_pdb_inputs(pdb_str=pdb_str_1)</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "./tst_sa.py", line 108, in get_pdb_inputs</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> rama_potential=None, log = None)</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> mon_lib_srv = mmtbx.monomer_library.server.server()</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> list_cif = mon_lib_list_cif()</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> strict=strict)</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> self.cif = read_cif(file_name=self.path)</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> return iotbx.cif.reader(file_path=file_name, strict=False).model()</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> raise CifParserError(self.parser.parser_errors()[0])</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco">CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> near global</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> : unexpected input...</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco"> expected one of : Actually dude, we didn't seem to be expecting anything here, or at least</font></div></div></div></div><div><div><div><div><font class="Apple-style-span" face="Monaco">I could not work out what I was expecting, like so many of us these days!</font></div></div></div></div></blockquote><div><div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4"><br></font></div><div><font class="Apple-style-span" size="4">James</font></div><div><font class="Apple-style-span" size="4"><br></font></div></div><br></div></body></html>