Hi Rajesh,
Yes, you can use your high resolution structures to generate reference
model restraints. Currently each reference chain must be in the same file
with a unique chain ID, so you'll need to combine your multiple reference
files into one and then use that. I am working on adding support for
multiple files, which I hope to have in place soon.
To use the reference model, you need to add these parameters:
refinement {
main {
reference_model_restraints = True
}
reference_model {
file = reference.pdb
}
}
The chains should be matched automatically, but you can specify a
selection, too. If you run into any trouble getting this working, please
let me know.
Thanks,
Jeff
On Thu, Mar 22, 2012 at 2:28 PM, Rajesh kumar
Dear All, In a case where we have a complex of two proteins and a peptide and for all three high resolution individual or homologue structures are available.
I am curious, if it is possible to use individual protein's high-resolution structure for reference model restraints? In similar way, could we use two individual structure as restraints for complex structure?
Thanks Rajesh
Date: Thu, 22 Mar 2012 19:59:14 +0100 From: [email protected] To: [email protected] Subject: [phenixbb] error generating output file overal_best pdb
Dear Phenix users,
I have been running Phenix_Autobuild successfully for the last houra. The program generates the corresponding Autobuild_run_** folders as usually, however I got an error message when the program was trying to generate the overal_best.pdb file after the Autobuild cycle 3.
I copy below the error message that I got, thank you in advance for any help:
OSError : [Errno 2] No such file or directory: '/user/palencia'
Traceback (most recent call last): File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Home/Jobs.py",
line 170, in OnTimer self.project.refresh_detached_jobs() File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Tracking.py",
line 72, in refresh_detached_jobs tmp_dir = self.get_tmp_dir() File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/phenix/tracking/project.py",
line 97, in get_tmp_dir os.makedirs(tmp_dir) File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
line 150, in makedirs makedirs(head, mode) File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
line 150, in makedirs makedirs(head, mode) File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
line 150, in makedirs makedirs(head, mode) File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
line 150, in makedirs makedirs(head, mode) File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
line 150, in makedirs makedirs(head, mode) File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
line 150, in makedirs makedirs(head, mode) File
"/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
line 157, in makedirs mkdir(name, mode) OSError: [Errno 2] No such file or directory: '/user/palencia'
Platform info: __FILE__ =
/net/anaconda/scratch1/phenix/phenix-1.7.3-928/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Dec 6 2011 __TIME__ = 04:18:10 __x86_64__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.5 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.18-238.9.1.el5-x86_64-with-redhat-5.7-Final platform.architecture(): ('64bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 24 Memory total: 25,263,722,496 Memory free: 20,157,317,120 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Ã…
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