[phenixbb] reference structure restaints

Rajesh kumar ccp4_sc at hotmail.com
Thu Mar 22 15:21:30 PDT 2012


Dear Jeff,

Thanks for the help. I will try and get back to you if I run into problems.

Rajesh

Sent from my iPhone

On Mar 22, 2012, at 4:35 PM, "Jeff Headd" <jjheadd at lbl.gov> wrote:

> 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 <ccp4_sc at hotmail.com> wrote:
> 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…
> > 
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> 
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