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

Pavel Afonine pafonine at lbl.gov
Thu Apr 20 17:54:28 PDT 2017


No, no tools to abuse file formats, sorry 🙂
Pavel

On Apr 20, 2017 3:10 PM, "Reza Khayat" <rkhayat at ccny.cuny.edu> wrote:

> 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 <phenixbb-bounces at phenix-
> online.org> on behalf of ludovic.pecqueur at college-de-france.fr <
> ludovic.pecqueur at college-de-france.fr>
> *Sent:* Tuesday, November 8, 2016 10:28 AM
> *To:* Nigel Moriarty
> *Cc:* 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> 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 <947%2020%2082%2035>
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov <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> 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_sr
>> c_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/Ca
>> rtesianSampler.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/cifp
>> arse/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/protocol
>> s/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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