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

It can be done with a very simple python or perl script that parses both the PDB file and the file with CC values, and then replaces corresponding B-factors with CC. 

Oleg

 
Oleg Borbulevych, Ph.D.
Staff Scientist
QuantumBio, Inc.
2790 W. College Ave.
State College, PA 16801
E-mail: [email protected], [email protected]
Linkedin Professional Profile: http://www.linkedin.com/pub/oleg-borbulevych/22/454/b80


-----Original Message-----
From: "Tim Gruene" 
Sent: Friday, April 21, 2017 3:59am
To: "PHENIX user mailing list" 
Subject: Re: [phenixbb] Calculating CC and inserting it into B-factor

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Unsubscribe: [email protected] Reza,

this could be achieved with some command line tools. 
If you have the CC per atom in the same order as the atoms in the PDB file,

I would strip the PDB file off anything but the ATOM cards, remove everything 
per line beyond the occupancy and paste the two files together. 
You can add the header afterwards.

Best regards,
Tim

On Thursday 20 April 2017 10:07:11 PM Reza Khayat 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: [email protected]
>  on behalf of
> [email protected]
>  Sent: Tuesday, November 8, 2016
> 10:28 AM
> To: Nigel Moriarty
> Cc: [email protected]
> 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
> > 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 :
> [email protected] Fax   : 510-486-5909      
> Web  :
> CCI.LBL.gov _&d=DgIFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMx
> gH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=j
> 9KRfzD1wS0qoGc9M1kgp2NfeTcgpdZ63qi0nzh4Wdw&e= >
> 
> On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur
>  rance.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 full-2Doptions-2Dlist.md_&d=DgIFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtI
> MGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7e
> v5xmpm7vPsNVtOHsU1GA&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 nt.com/v2/url?u=http-3A__cartesiansampler.cc&d=DgIFAw&c=4NmamNZG3KTnUCoC6Ino
> LJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=Cclp
> QbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=s1h3iBFqQztjSfFsFE-tj-D2VWkeV7BFeD
> kTFNrnHnw&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_mo
> vers.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/sqlite
> 3.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_20
> 16.13.58602_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/CifDataInf
> o.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/CifFileRea
> dDef.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentC
> hild.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserB
> ase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner
> Base.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.o
> s
> 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/DICParserB
> ase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner
> Base.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_vec
> tor.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChil
> d.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/RcsbPlatfo
> rm.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.o
> s
> 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/Pheni
> xInterface.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/XtalM
> LEnergy.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_m
> overs.os] Error 1 scons: ***
> [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/Phen
> ixInterface.os] Error 1 scons: ***
> [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/Xtal
> MLEnergy.os] Error 1 scons: building terminated because of errors.
> 
> 
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- persoenlich -
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