[phenixbb] Calculating CC and inserting it into B-factor

Bjarte Aarmo Lund bjarte.lund at uit.no
Fri Apr 21 01:20:38 PDT 2017


Dear Reza,


Without having tried it, there is a pymol-script for replacing the B-factor values:
https://pymolwiki.org/index.php/Load_new_B-factors

Good luck,

Kind regards,

Bjarte Aarmo Lund
PhD candidate
UiT - The arctic university of Norway

From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Reza Khayat
Sent: 21. april 2017 00:07
Cc: phenixbb at phenix-online.org
Subject: [phenixbb] Calculating CC and inserting it into B-factor


Hi,



Is there a phenix program that will insert the calculated CC (between the PDB and map) into the B-factor column? Thanks.



Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
________________________________
From: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> <phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>> on behalf of ludovic.pecqueur at college-de-france.fr<mailto:ludovic.pecqueur at college-de-france.fr> <ludovic.pecqueur at college-de-france.fr<mailto:ludovic.pecqueur at college-de-france.fr>>
Sent: Tuesday, November 8, 2016 10:28 AM
To: Nigel Moriarty
Cc: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Cannot compile rosetta interface Centos 7 with 1.11.1

Dear Nigel,

Switching to rosetta 3.7 did the trick.

Thanks a lot for the tip.

Ludovic.


On 07 Nov 2016, at 18:39, Nigel Moriarty <nwmoriarty at lbl.gov<mailto:nwmoriarty at lbl.gov>> wrote:

Ludovic

Can you move to Rosetta 3.7 and let me know if it still fails?

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov<mailto:NWMoriarty at lbl.gov>
Fax   : 510-486-5909       Web  : CCI.LBL.gov<https://urldefense.proofpoint.com/v2/url?u=http-3A__cci.lbl.gov_&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=j9KRfzD1wS0qoGc9M1kgp2NfeTcgpdZ63qi0nzh4Wdw&e=>

On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur <ludovic.pecqueur at college-de-france.fr<mailto:ludovic.pecqueur at college-de-france.fr>> wrote:
Dear Phenix developers,

I installed the latest phenix version today (1.11.1-2575) on Centos 7.2
I have rosetta_2016.13.58602

When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).

When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.

If you have any idea of the change between the two versions leading to this issue.

Thank you for your help,

Ludovic.

########################
Error message:

Substituting phenix.python into build shell scripts
  update_options.sh
  update_ResidueType_enum_files.sh
/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source

  ~> phenix.python scons.py bin mode=release extras=python  -j 8

scons: Reading SConscript files ...
Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Done. (0.0 seconds)
file ./options.dox being updated
file ./full-options-list.md<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=> being updated
Number of option files updated: 2
Total 3657 options.
Finished updating ResidueProperty code -- no changes needed
Finished updating VariantType code -- no changes needed
scons: done reading SConscript files.
scons: Building targets ...
g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.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_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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/CartesianSampler.cc<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=>
In file included from src/protocols/hybridization/CartesianSampler.cc:17:0:
src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory
 #include "Python.h"
                    ^
compilation terminated.
g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/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_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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_movers.cc
In file included from src/protocols/cryst/cryst_movers.cc:16:0:
src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory
 #include "Python.h"
                    ^
compilation terminated.
gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil
g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.!
 os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil
g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/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_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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/PhenixInterface.cc
In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0:
src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory
 #include "Python.h"
                    ^
compilation terminated.
g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/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_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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/XtalMLEnergy.cc
In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0:
src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory
 #include "Python.h"
                    ^
compilation terminated.
scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os] Error 1
scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1
scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1
scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1
scons: building terminated because of errors.


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