[phenixbb] Cryo-EM image reconstruction pixle size refinement

Reza Khayat rkhayat at ccny.cuny.edu
Mon Apr 3 14:30:31 PDT 2017 

Hi,


Is there a method to refine the pixel size of an image reconstruction if the PDB has been docked in? 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<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<http://cci.lbl.gov/>

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<http://full-options-list.md/> 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<http://cartesiansampler.cc>
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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