<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><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">On Apr 10, 2013, at 11:46 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">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><font class="Apple-style-span" size="4"><br></font><div><font class="Apple-style-span" size="4">I downloaded this library, but its failing. Do you know what I'm doing wrong?</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><div><div><font class="Apple-style-span" face="Monaco">chernev 50% cctbx.python ./tst_sa.py</font></div><div><font class="Apple-style-span" face="Monaco">Traceback (most recent call last):</font></div><div><font class="Apple-style-span" face="Monaco"> File "./tst_sa.py", line 267, in <module></font></div><div><font class="Apple-style-span" face="Monaco"> exercise_1()</font></div><div><font class="Apple-style-span" face="Monaco"> File "./tst_sa.py", line 122, in exercise_1</font></div><div><font class="Apple-style-span" face="Monaco"> pi = get_pdb_inputs(pdb_str=pdb_str_1)</font></div><div><font class="Apple-style-span" face="Monaco"> File "./tst_sa.py", line 108, in get_pdb_inputs</font></div><div><font class="Apple-style-span" face="Monaco"> rama_potential=None, log = None)</font></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><font class="Apple-style-span" face="Monaco"> mon_lib_srv = mmtbx.monomer_library.server.server()</font></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><font class="Apple-style-span" face="Monaco"> geostd_list_cif_obj = geostd_list_cif()</font></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><font class="Apple-style-span" face="Monaco"> strict=strict)</font></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><font class="Apple-style-span" face="Monaco"> + ", ".join(mon_lib_env_vars))</font></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><font class="Apple-style-span" face="Monaco">chernev 51% ls $MMTBX_CCP4_MONOMER_LIB/</font></div><div><font class="Apple-style-span" face="Monaco">total 10248</font></div><div><font class="Apple-style-span" face="Monaco"> 0 0/ 8 COPYING 0 g/ 0 n/ 0 u/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 1/ 0 a/ 0 h/ 0 o/ 0 v/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 2/ 0 b/ 0 i/ 0 p/ 0 w/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 3/ 0 c/ 0 j/ 2436 pdb_alt_names.txt 0 x/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 4/ 0 d/ 0 k/ 8 pdb_v2to3.py 0 y/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 5/ 4 dnarna_basepairs.txt 0 l/ 0 q/ 0 z/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 6/ 4 dnarna_basepairs_2.txt 0 list/ 0 r/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 7/ 0 e/ 0 m/ 0 s/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 8/ 104 ener_lib.cif 1340 mon_lib_ind.cif 0 t/</font></div><div><font class="Apple-style-span" face="Monaco"> 0 9/ 0 f/ 6340 mon_lib_ind2.cif 4 template_link.pdb</font></div><div><font class="Apple-style-span" face="Monaco">chernev 52% echo $MMTBX_CCP4_MONOMER_LIB/</font></div><div><font class="Apple-style-span" face="Monaco">/usr/local/refmac-v5.39/monomers/</font></div></div><div><font class="Apple-style-span" face="Monaco"><br></font></div></body></html>