[phenixbb] Custom restraints editor

[Kristof Van Hecke]

Dear,

When I try to define additional 'planarity' restraints via the 'Custom  
restraints editor', I get the following error (see below):
(I'm using the Phenix nightly build dev-1148 on a Mac Book Pro, OS X  
10.5.8, but had the same problem with the official release version 1.8)
I also tried to add these additional restraints to my restraints .cif  
file, but then rmsd values increase to unreasonably high values.
(I just want to keep 2 chlorine atoms on a phenyl ring better in the  
same plane)

Any ideas please..?

Thank you very much

Kristof Van Hecke


---------------------
untimeError : Syntax error: missing closing quote (python_object, line  
1)

Traceback (most recent call last):
   File "/Applications/phenix-dev-1148/phenix/wxGUI2/Programs/Refine/ 
Dialogs.py", line 296, in OnUpdate
     new_phil = self.GetPhilObject()
   File "/Applications/phenix-dev-1148/cctbx_project/wxtbx/ 
custom_restraints.py", line 646, in GetPhilObject
     new_phil =  
self._index.master_phil.format(python_object=self._params)
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 1714, in format
     result.append(object.format(sub_python_object))
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 1714, in format
     result.append(object.format(sub_python_object))
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 1714, in format
     result.append(object.format(sub_python_object))
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 1727, in format
     result.append(object.format(sub_python_object_i))
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 1727, in format
     result.append(object.format(sub_python_object_i))
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 1094, in format
     words = type_as_words(python_object=python_object, master=self)
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 151, in as_words
     source_info="python_object")
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
__init__.py", line 60, in tokenize_value_literal
     tokenizer.settings(contiguous_word_characters="")]))
   File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ 
tokenizer.py", line 249, in next
     where_str(O.source_info, char_iter.line_number)))
RuntimeError: Syntax error: missing closing quote (python_object, line  
1)



Platform info:
__FILE__ = /net/patchnose/scratch1/phenix/phenix-dev-1148/ 
cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Sep  3 2012
__TIME__ = 06:05:56
__i386__
__APPLE_CC__ = 5367
__GNUC__ = 4
__GNUC_MINOR__ = 0
__GNUC_PATCHLEVEL__ = 1
boost::python::cxxabi_cxa_demangle_is_broken(): false
__GXX_WEAK__ = 1
__VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367)
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_51
PY_VERSION = 2.7.3
PYTHON_API_VERSION = 1013
sizeof(bool) = 1
sizeof(short) = 2
sizeof(int) = 4
sizeof(long) = 4
sizeof(std::size_t) = 4
sizeof(void*) = 4
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
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
boost/TAG: 79991
os.name: posix
sys.platform: darwin
sys.byteorder: little
platform.platform(): Darwin-9.8.0-i386-32bit
platform.architecture(): ('32bit', '')
floating_point_exceptions.division_by_zero_trapped: False
floating_point_exceptions.invalid_trapped: False
floating_point_exceptions.overflow_trapped: False
number of processors: 2
Memory total:  4,294,967,296
Memory free:         unknown
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 = √Ö