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<p>Hi,<br>
</p>
<p><br>
</p>
<p>Is there a phenix program that will insert the calculated&nbsp;CC&nbsp;(between the PDB and map) into the B-factor column? Thanks.</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza&nbsp;<br>
</p>
<p><br>
</p>
<div id="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
Reza Khayat, PhD
<div>Assistant Professor&nbsp;</div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> phenixbb-bounces@phenix-online.org &lt;phenixbb-bounces@phenix-online.org&gt; on behalf of ludovic.pecqueur@college-de-france.fr &lt;ludovic.pecqueur@college-de-france.fr&gt;<br>
<b>Sent:</b> Tuesday, November 8, 2016 10:28 AM<br>
<b>To:</b> Nigel Moriarty<br>
<b>Cc:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Cannot compile rosetta interface Centos 7 with 1.11.1</font>
<div>&nbsp;</div>
</div>
<div>Dear Nigel,
<div class=""><br class="">
</div>
<div class="">Switching to rosetta 3.7 did the trick.</div>
<div class=""><br class="">
</div>
<div class="">Thanks a lot for the tip.</div>
<div class=""><br class="">
</div>
<div class="">Ludovic.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 07 Nov 2016, at 18:39, Nigel Moriarty &lt;<a href="mailto:nwmoriarty@lbl.gov" class="">nwmoriarty@lbl.gov</a>&gt; wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Ludovic
<div class=""><br class="">
</div>
<div class="">Can you move to Rosetta 3.7 and let me know if it still fails?</div>
</div>
<div class="gmail_extra"><br clear="all" class="">
<div class="">
<div class="gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">Cheers
<div class=""><br class="">
</div>
<div class="">Nigel
<div class=""><br class="">
</div>
<div class="">---</div>
<div class="">Nigel W. Moriarty<br class="">
Building 33R0349,&nbsp;Molecular Biophysics and Integrated Bioimaging</div>
<div class="">Lawrence Berkeley National Laboratory<br class="">
Berkeley, CA 94720-8235<br class="">
Phone : 510-486-5709&nbsp; &nbsp;&nbsp; Email : <a href="mailto:NWMoriarty@lbl.gov" class="">NWMoriarty@LBL.gov</a><br class="">
Fax&nbsp;&nbsp; : 510-486-5909&nbsp; &nbsp; &nbsp;&nbsp; Web&nbsp; : <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__cci.lbl.gov_&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=j9KRfzD1wS0qoGc9M1kgp2NfeTcgpdZ63qi0nzh4Wdw&e=" target="_blank" class="">
CCI.LBL.gov</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
<div class="gmail_quote">On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur <span dir="ltr" class="">
&lt;<a href="mailto:ludovic.pecqueur@college-de-france.fr" target="_blank" class="">ludovic.pecqueur@college-de-france.fr</a>&gt;</span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
Dear Phenix developers,<br class="">
<br class="">
I installed the latest phenix version today (1.11.1-2575) on Centos 7.2<br class="">
I have rosetta_2016.13.58602<br class="">
<br class="">
When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).<br class="">
<br class="">
When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.<br class="">
<br class="">
If you have any idea of the change between the two versions leading to this issue.<br class="">
<br class="">
Thank you for your help,<br class="">
<br class="">
Ludovic.<br class="">
<br class="">
########################<br class="">
Error message:<br class="">
<br class="">
Substituting phenix.python into build shell scripts<br class="">
&nbsp; update_options.sh<br class="">
&nbsp; update_ResidueType_enum_files.<wbr class="">sh<br class="">
/usr/local/PROGRAMS/ROSETTA/<wbr class="">PHENIX_Rosetta_refine/rosetta_<wbr class="">src_2016.13.58602_bundle/main/<wbr class="">source<br class="">
<br class="">
&nbsp; ~&gt; phenix.python scons.py bin mode=release extras=python&nbsp; -j 8<br class="">
<br class="">
scons: Reading SConscript files ...<br class="">
Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local)<br class="">
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_<wbr class="">FILESYSTEM not set).<br class="">
Done. (0.0 seconds)<br class="">
file ./options.dox being updated<br class="">
file ./<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__full-2Doptions-2Dlist.md_&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=QQ-WkxsPQmBAfCDpGq6Kiqi769wKOQiKKsMiZgaaIFs&e=" rel="noreferrer" target="_blank" class="">full-options-list.md</a> being updated<br class="">
Number of option files updated: 2<br class="">
Total 3657 options.<br class="">
Finished updating ResidueProperty code -- no changes needed<br class="">
Finished updating VariantType code -- no changes needed<br class="">
scons: done reading SConscript files.<br class="">
scons: Building targets ...<br class="">
g&#43;&#43; -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/hybridization/<wbr class="">CartesianSampler.os -c -std=c&#43;&#43;98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem
 external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY
 -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
 -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/<wbr class=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__cartesiansampler.cc&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=s1h3iBFqQztjSfFsFE-tj-D2VWkeV7BFeDkTFNrnHnw&e=" class="">CartesianSampler.cc</a><br class="">
In file included from src/protocols/hybridization/<wbr class="">CartesianSampler.cc:17:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
&nbsp;#include &quot;Python.h&quot;<br class="">
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^<br class="">
compilation terminated.<br class="">
g&#43;&#43; -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/cryst/cryst_movers.<wbr class="">os -c -std=c&#43;&#43;98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/
 -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
 -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0
 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_<wbr class="">movers.cc<br class="">
In file included from src/protocols/cryst/cryst_<wbr class="">movers.cc:16:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
&nbsp;#include &quot;Python.h&quot;<br class="">
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^<br class="">
compilation terminated.<br class="">
gcc -o build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">libsqlite3.so -shared build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib
 -lpython2.7 -ldl -lpthread -lutil<br class="">
g&#43;&#43; -o build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">libcifparse.so -Wl,-rpath=/usr/local/<wbr class="">PROGRAMS/ROSETTA/PHENIX_<wbr class="">Rosetta_refine/rosetta_src_<wbr class="">2016.13.58602_bundle/main/<wbr class="">source/build/external/release/<wbr class="">linux/3.10/64/x86/gcc/4.8/<wbr class="">python
 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/BlockIO.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifDataInfo.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifExcept.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifFile.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifFileReadDef.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifParentChild.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifParserBase.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifScannerBase.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifString.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DataInfo.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DicFile.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICParserBase.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICScannerBase.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/Exceptions.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/GenCont.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/GenString.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/ISTable.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/ITTable.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/mapped_ptr_vector.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/mapped_vector.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/ParentChild.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/RcsbFile.!<br class="">
&nbsp;os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/RcsbPlatform.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/Serializer.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/TableFile.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/TTable.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifParser.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifScanner.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICParser.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICScanner.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regcomp.os
 build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regerror.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regexec.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regfree.os
 -Lexternal/lib -Lbuild/external/release/<wbr class="">linux/3.10/64/x86/gcc/4.8/<wbr class="">python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil<br class="">
g&#43;&#43; -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/PhenixInterface.<wbr class="">os -c -std=c&#43;&#43;98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/
 -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
 -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0
 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/<wbr class="">PhenixInterface.cc<br class="">
In file included from src/core/scoring/cryst/<wbr class="">PhenixInterface.cc:15:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
&nbsp;#include &quot;Python.h&quot;<br class="">
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^<br class="">
compilation terminated.<br class="">
g&#43;&#43; -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/XtalMLEnergy.os -c -std=c&#43;&#43;98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall
 -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
 -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0
 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/<wbr class="">XtalMLEnergy.cc<br class="">
In file included from src/core/scoring/cryst/<wbr class="">XtalMLEnergy.cc:16:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
&nbsp;#include &quot;Python.h&quot;<br class="">
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^<br class="">
compilation terminated.<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/hybridization/<wbr class="">CartesianSampler.os] Error 1<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/cryst/cryst_movers.<wbr class="">os] Error 1<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/PhenixInterface.<wbr class="">os] Error 1<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/XtalMLEnergy.os] Error 1<br class="">
scons: building terminated because of errors.<br class="">
<br class="">
<br class="">
______________________________<wbr class="">_________________<br class="">
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