<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"><br></font><div><div><font class="Apple-style-span" size="4">On Apr 10, 2013, at 11:46 PM, Nathaniel Echols wrote:</font></div><font class="Apple-style-span" size="4"><br class="Apple-interchange-newline"></font><blockquote type="cite"><div dir="ltr"><div class="gmail_extra"><font class="Apple-style-span" size="4">On Wed, Apr 10, 2013 at 3:58 PM, James Stroud <span dir="ltr"><<a href="mailto:xtald00d@gmail.com" target="_blank">xtald00d@gmail.com</a>></span> wrote:</font><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div><div><div><font class="Apple-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></div></div></blockquote><div><font class="Apple-style-span" size="4"><br></font></div><div style=""><font class="Apple-style-span" size="4">Well, for what it's worth, I just nuked my installation and downloaded the same thing minus ARP/wARP, and now I have the same header as you reported. Will continue digging tomorrow, but I suspect that either the updates will eventually fix the problem, or something has changed in the installer (although using an older version of the monomer library seems like a weird choice).</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">I actually iterated through updates until I there were no more. I think I over-shot the sweet spot, though:</font></div><div><font class="Apple-style-span" size="4"><br></font></div></div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div><div><font class="Apple-style-span" face="Monaco">chernev 13% setenv MMTBX_CCP4_MONOMER_LIB /usr/local/ccp4-6.3.0/lib/data/monomers/</font></div></div></div><div><div><div><font class="Apple-style-span" face="Monaco">chernev 14% cctbx.python ./tst_sa.py</font></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><font class="Apple-style-span" face="Monaco"> File "./tst_sa.py", line 267, in <module></font></div></div></div><div><div><div><font class="Apple-style-span" face="Monaco"> exercise_1()</font></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><font class="Apple-style-span" face="Monaco"> pi = get_pdb_inputs(pdb_str=pdb_str_1)</font></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><font class="Apple-style-span" face="Monaco"> rama_potential=None, log = None)</font></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><font class="Apple-style-span" face="Monaco"> mon_lib_srv = mmtbx.monomer_library.server.server()</font></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 226, in __init__</font></div></div></div><div><div><div><font class="Apple-style-span" face="Monaco"> geostd_list_cif_obj = geostd_list_cif()</font></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 69, in geostd_list_cif</font></div></div></div><div><div><div><font class="Apple-style-span" face="Monaco"> strict=strict)</font></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 56, in __init__</font></div></div></div><div><div><div><font class="Apple-style-span" face="Monaco"> + ", ".join(mon_lib_env_vars))</font></div></div></div><div><div><div><font class="Apple-style-span" face="Monaco">mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON</font></div></div></div></blockquote><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">Also note that you can download the monomer library as a separate package from Garib Murshudov's home page:</font></div><div style=""><font class="Apple-style-span" size="4"><br></font></div><div style=""><font class="Apple-style-span" size="4"><a href="http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/">http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/</a> [ click "software" --> "Refmac5" --> "Dictionary of ligands" ]</font></div>
<div style=""><font class="Apple-style-span" size="4"><br></font></div><div style=""><font class="Apple-style-span" size="4">and this looks like it is formatted correctly.</font></div></div></div></div></blockquote><div><br></div><div><br></div><div><font class="Apple-style-span" size="4">I'll give this one a try.</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><br></div><div><br></div><br><blockquote type="cite"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div style=""><font class="Apple-style-span" size="4"><br></font></div><div style=""><font class="Apple-style-span" size="4">-Nat </font></div></div></div></div></blockquote></div></body></html>