[phenixbb] reference structure restaints

[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: palencia at embl.fr
> To: phenixbb at phenix-online.org
> 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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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
 		 	   		  
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