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<body class='hmmessage'><div dir='ltr'>Hi,<div><br></div><div>the CIF parser will report this error if any of the CIF items is outside data_ or save_ blocks. So you need to change 'global' to 'data_global' to prevent this error.</div><div><br></div><div>Cheers,</div><div><br></div><div>o<br><br><div><div id="SkyDrivePlaceholder"></div><hr id="stopSpelling">From: xtald00d@gmail.com<br>Date: Wed, 10 Apr 2013 16:58:40 -0600<br>To: cctbxbb@phenix-online.org<br>Subject: Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility<br><br><font class="ecxApple-style-span" size="4">Hi Nat,</font><div><font class="ecxApple-style-span" size="4"><br></font><div><div><font class="ecxApple-style-span" size="4">On Apr 10, 2013, at 4:44 PM, Nathaniel Echols wrote:</font></div><blockquote><div dir="ltr"><font class="ecxApple-style-span" size="4">PS. Actually, there are other differences:</font><div><font class="ecxApple-style-span" size="4"><br></font></div><div><div><font class="ecxApple-style-span" size="4">global_</font></div><div><font class="ecxApple-style-span" size="4">_lib_name mon_lib</font></div><div><font class="ecxApple-style-span" size="4">_lib_version 5.39</font></div><div><font class="ecxApple-style-span" size="4">_lib_update 06/11/12</font></div></div><div><font class="ecxApple-style-span" size="4"><br></font></div><div style=""><font class="ecxApple-style-span" size="4">
So it's three months newer than the one you're using. Have you run the CCP4 updater?</font></div></div></blockquote><div><font class="ecxApple-style-span" size="4"><br></font></div><div><font class="ecxApple-style-span" size="4">Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg</font></div><div><font class="ecxApple-style-span" size="4"><br></font></div><div><font class="ecxApple-style-span" size="4">I just ran the updater (bin/update) but it didn't touch mon_lib_list.cif even though it reported to complete successfully. If I have more cif problems, I'll download the latest ccp4 sources and see what happens when I build from scratch.</font></div><div><font class="ecxApple-style-span" size="4"><br></font></div><div><font class="ecxApple-style-span" size="4">James</font></div><div><font class="ecxApple-style-span" size="4"><br></font></div><div><br></div><br><blockquote><div class="ecxgmail_extra"><br><div class="ecxgmail_quote">On Wed, Apr 10, 2013 at 3:38 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex;"><div dir="ltr">Actually, I think there may be a problem with your CCP4 installation - the exact same file on my computer starts with "global_", while yours lacks the trailing underscore, and editing mine to match reproduces the crash. With the underscore in place it should work (assuming nothing else has changed).</div>
<div class="ecxgmail_extra"><br><br><div class="ecxgmail_quote"><div><div class="h5">On Wed, Apr 10, 2013 at 3:28 PM, James Stroud <span dir="ltr"><<a href="mailto:xtald00d@gmail.com" target="_blank">xtald00d@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="ecxgmail_quote" style="border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex;"><div><div class="h5">
<div style="word-wrap:break-word;"><font size="4">Hi Nat,</font><div><font size="4"><br></font></div><div><font size="4"><br></font><div><div><div><font size="4">On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:</font></div>
<blockquote><div dir="ltr"><div class="ecxgmail_extra"><div class="ecxgmail_quote"><div><font 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 size="4"><br></font></div></div><div><font size="4">Yes, that is the script I'm running.</font></div><div><div><font size="4"><br></font></div><font size="4"><br></font><blockquote>
<div dir="ltr"><div class="ecxgmail_extra"><div class="ecxgmail_quote"><div><font 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 size="4"><br></font></div></div><div><font size="4">Here's the results:</font></div><div><font size="4"><br></font></div></div></div><blockquote style="border:none;padding:0px;">
<div><div><div><div><font face="Monaco">% setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1</font></div><div><font face="Monaco">% cctbx.python ./tst_sa.py</font></div></div></div></div><div><div><div><div><font face="Monaco">Traceback (most recent call last):</font></div>
</div></div></div><div><div><div><div><font face="Monaco"> File "./tst_sa.py", line 267, in <module></font></div></div></div></div><div><div><div><div><font face="Monaco"> exercise_1()</font></div></div>
</div></div><div><div><div><div><font face="Monaco"> File "./tst_sa.py", line 122, in exercise_1</font></div></div></div></div><div><div><div><div><font face="Monaco"> pi = get_pdb_inputs(pdb_str=pdb_str_1)</font></div>
</div></div></div><div><div><div><div><font face="Monaco"> File "./tst_sa.py", line 108, in get_pdb_inputs</font></div></div></div></div><div><div><div><div><font face="Monaco"> rama_potential=None, log = None)</font></div>
</div></div></div><div><div><div><div><font 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 face="Monaco"> mon_lib_srv = mmtbx.monomer_library.server.server()</font></div></div></div></div><div><div><div><div><font 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 face="Monaco"> list_cif = mon_lib_list_cif()</font></div></div></div></div><div><div><div><div><font 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 face="Monaco"> strict=strict)</font></div></div></div></div><div><div><div><div><font 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 face="Monaco"> self.cif = read_cif(file_name=self.path)</font></div></div></div></div><div><div><div><div><font 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 face="Monaco"> return iotbx.cif.reader(file_path=file_name, strict=False).model()</font></div></div></div></div><div><div><div><div><font 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 face="Monaco"> raise CifParserError(self.parser.parser_errors()[0])</font></div></div></div></div><div><div><div><div><div><font 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 face="Monaco"> near global</font></div></div></div></div><div><div><div><div><font face="Monaco"> : unexpected input...</font></div></div></div></div><div><div><div><div>
<font 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 face="Monaco">I could not work out what I was expecting, like so many of us these days!</font></div>
</div></div></div></div></blockquote><span><font color="#888888"><div><div><div><font size="4"><br></font></div><div><font size="4"><br></font></div><div><font size="4">James</font></div><div><font size="4"><br>
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