<div dir="auto">No, no tools to abuse file formats, sorry 🙂<div dir="auto">Pavel</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Apr 20, 2017 3:10 PM, "Reza Khayat" <<a href="mailto:rkhayat@ccny.cuny.edu">rkhayat@ccny.cuny.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi,<br>
</p>
<p><br>
</p>
<p>Is there a phenix program that will insert the calculated CC (between the PDB and map) into the B-factor column? Thanks.</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza <br>
</p>
<p><br>
</p>
<div id="m_4119835887233453470Signature">
<div name="divtagdefaultwrapper">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<div style="word-wrap:break-word">
<hr style="display:inline-block;width:98%">
<div id="m_4119835887233453470divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<wbr>online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<wbr>online.org</a>> on behalf of <a href="mailto:ludovic.pecqueur@college-de-france.fr" target="_blank">ludovic.pecqueur@college-de-<wbr>france.fr</a> <<a href="mailto:ludovic.pecqueur@college-de-france.fr" target="_blank">ludovic.pecqueur@college-de-<wbr>france.fr</a>><br>
<b>Sent:</b> Tuesday, November 8, 2016 10:28 AM<br>
<b>To:</b> Nigel Moriarty<br>
<b>Cc:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] Cannot compile rosetta interface Centos 7 with 1.11.1</font>
<div> </div>
</div>
<div>Dear Nigel,
<div><br>
</div>
<div>Switching to rosetta 3.7 did the trick.</div>
<div><br>
</div>
<div>Thanks a lot for the tip.</div>
<div><br>
</div>
<div>Ludovic.</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 07 Nov 2016, at 18:39, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>> wrote:</div>
<br class="m_4119835887233453470Apple-interchange-newline">
<div>
<div dir="ltr">Ludovic
<div><br>
</div>
<div>Can you move to Rosetta 3.7 and let me know if it still fails?</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="m_4119835887233453470gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">Cheers
<div><br>
</div>
<div>Nigel
<div><br>
</div>
<div>---</div>
<div>Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div>
<div>Lawrence Berkeley National Laboratory<br>
Berkeley, CA <a href="tel:947%2020%2082%2035" value="+34947208235" target="_blank">94720-8235</a><br>
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@lbl.gov" target="_blank">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <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">
CCI.LBL.gov</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur <span dir="ltr">
<<a href="mailto:ludovic.pecqueur@college-de-france.fr" target="_blank">ludovic.pecqueur@college-de-<wbr>france.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Phenix developers,<br>
<br>
I installed the latest phenix version today (1.11.1-2575) on Centos 7.2<br>
I have rosetta_2016.13.58602<br>
<br>
When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).<br>
<br>
When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.<br>
<br>
If you have any idea of the change between the two versions leading to this issue.<br>
<br>
Thank you for your help,<br>
<br>
Ludovic.<br>
<br>
########################<br>
Error message:<br>
<br>
Substituting phenix.python into build shell scripts<br>
update_options.sh<br>
update_ResidueType_enum_files.<wbr>sh<br>
/usr/local/PROGRAMS/ROSETTA/PH<wbr>ENIX_Rosetta_refine/rosetta_sr<wbr>c_2016.13.58602_bundle/main/so<wbr>urce<br>
<br>
~> phenix.python scons.py bin mode=release extras=python -j 8<br>
<br>
scons: Reading SConscript files ...<br>
Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local)<br>
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYST<wbr>EM not set).<br>
Done. (0.0 seconds)<br>
file ./options.dox being updated<br>
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">full-options-list.md</a> being updated<br>
Number of option files updated: 2<br>
Total 3657 options.<br>
Finished updating ResidueProperty code -- no changes needed<br>
Finished updating VariantType code -- no changes needed<br>
scons: done reading SConscript files.<br>
scons: Building targets ...<br>
g++ -o build/src/release/linux/3.10/6<wbr>4/x86/gcc/4.8/python/protocols<wbr>/hybridization/CartesianSample<wbr>r.os -c -std=c++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_MA<wbr>TH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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/<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=" target="_blank">Ca<wbr>rtesianSampler.cc</a><br>
In file included from src/protocols/hybridization/Ca<wbr>rtesianSampler.cc:17:0:<br>
src/core/scoring/cryst/PhenixI<wbr>nterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
g++ -o build/src/release/linux/3.10/6<wbr>4/x86/gcc/4.8/python/protocols<wbr>/cryst/cryst_movers.os -c -std=c++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_MA<wbr>TH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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_move<wbr>rs.cc<br>
In file included from src/protocols/cryst/cryst_move<wbr>rs.cc:16:0:<br>
src/core/scoring/cryst/PhenixI<wbr>nterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
gcc -o build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/libs<wbr>qlite3.so -shared build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/dbio<wbr>/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib
-lpython2.7 -ldl -lpthread -lutil<br>
g++ -o build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/libc<wbr>ifparse.so -Wl,-rpath=/usr/local/PROGRAMS<wbr>/ROSETTA/PHENIX_Rosetta_<wbr>refine/rosetta_src_2016.13.<wbr>58602_bundle/main/source/<wbr>build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python
-Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/BlockIO.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifDataInfo.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifExcept.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifFile.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifFileReadDef.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifParentChild.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifParserBase.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifScannerBase.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifString.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/DataInfo.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/DicFile.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/DICParserBase.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/DICScannerBase.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/Exceptions.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/GenCont.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/GenString.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/ISTable.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/ITTable.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/mapped_ptr_vector.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/mapped_vector.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/ParentChild.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/RcsbFile.!<br>
os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/RcsbPlatform.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/Serializer.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/TableFile.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/TTable.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifParser.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/CifScanner.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/DICParser.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/DICScanner.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/regcomp.os
build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/regerror.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/regexec.os build/external/release/linux/3<wbr>.10/64/x86/gcc/4.8/python/cifp<wbr>arse/regfree.os
-Lexternal/lib -Lbuild/external/release/linux<wbr>/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil<br>
g++ -o build/src/release/linux/3.10/6<wbr>4/x86/gcc/4.8/python/core/scor<wbr>ing/cryst/PhenixInterface.os -c -std=c++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_MA<wbr>TH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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/PhenixI<wbr>nterface.cc<br>
In file included from src/core/scoring/cryst/PhenixI<wbr>nterface.cc:15:0:<br>
src/core/scoring/cryst/PhenixI<wbr>nterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
g++ -o build/src/release/linux/3.10/6<wbr>4/x86/gcc/4.8/python/core/scor<wbr>ing/cryst/XtalMLEnergy.os -c -std=c++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_MA<wbr>TH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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/XtalMLE<wbr>nergy.cc<br>
In file included from src/core/scoring/cryst/XtalMLE<wbr>nergy.cc:16:0:<br>
src/core/scoring/cryst/PhenixI<wbr>nterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/protocol<wbr>s/hybridization/CartesianSampl<wbr>er.os] Error 1<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/protocol<wbr>s/cryst/cryst_movers.os] Error 1<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/core/sco<wbr>ring/cryst/PhenixInterface.os] Error 1<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/core/sco<wbr>ring/cryst/XtalMLEnergy.os] Error 1<br>
scons: building terminated because of errors.<br>
<br>
<br>
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