I'm having issues defining planarity restraints in a .edits file. When all four of the atoms in the plane are selected in a single planarity entry, refinement crashes. When I define a single atom in separate planarity restraint entries (as suggested by Nat), refinement doesn't crash, but the four atoms in the plane are treated as four one-atom planes (obviously useless). My previous correspondence is attached below.

Thanks,

Elwood

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Elwood A. Mullins
Research Associate
Department of Biochemistry
Purdue University
175 South University Street
West Lafayette, IN 47907-1612

Office: Biochemistry 29
Email: [email protected]
Tel: (765) 496-6814
Fax: (765) 494-7897
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

While refinement didn't crash, I'm not sure this worked. The .geo file lists the desired one plane with four atoms as four planes with one atom and rmsds = 0 with residuals = 0. It also seems impossible to define multiple planes in a .edits file with this syntax. The .geo and the .eff files are attached. I used the .edits file you sent me without modification.

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Elwood A. Mullins
Research Associate
Department of Biochemistry
Purdue University
175 South University Street
West Lafayette, IN 47907-1612

Office: Biochemistry 29
Tel: (765) 496-6814
Fax: (765) 494-7897
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

On Jul 22, 2010, at 2:45 PM, Nathaniel Echols wrote:

On Thu, Jul 22, 2010 at 2:41 PM, Elwood A. Mullins <[email protected]> wrote:
I'm loading a .edits file. It seems to work fine for the bond and angles. The file is attached.

Okay, it's just a syntax error - only bonds and angles have multiple atom selections (2 and 3, respectively).  For planarity, you define each plane separately, and you only need a single atom selection each, for all atoms in the plane.  Try the attached file with corrected parameters; let me know if this doesn't fix it.

thanks,
Nat



=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Elwood A. Mullins
Research Associate
Department of Biochemistry
Purdue University
175 South University Street
West Lafayette, IN 47907-1612

Office: Biochemistry 29
Tel: (765) 496-6814
Fax: (765) 494-7897
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

On Jul 22, 2010, at 2:20 PM, Nathaniel Echols wrote:

Sorry, I forgot to read your original message before I sent this.  I take it you're loading a .eff file into the GUI?  Could you please send me this file?

thanks,
Nat

On Thu, Jul 22, 2010 at 2:20 PM, Nathaniel Echols <[email protected]> wrote:
The atom selection for the planarity is missing - I suspect this is the problem.  What did you enter in the GUI?

On Thu, Jul 22, 2010 at 2:18 PM, Elwood A. Mullins <[email protected]> wrote:
I've tried a couple different sigma values (0.02 and 0.1) and received the same error. The .eff file is attached below.



=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Elwood A. Mullins
Research Associate
Department of Biochemistry
Purdue University
175 South University Street
West Lafayette, IN 47907-1612

Office: Biochemistry 29
Tel: (765) 496-6814
Fax: (765) 494-7897
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

On Jul 22, 2010, at 2:00 PM, Nathaniel Echols wrote:

Could you please send me the final .eff file written by the GUI?  (You can save a copy by clicking the Save button on the toolbar instead of running it.)  I suspect the problem is with incorrect sigma values, but it's hard to tell from this error, which is coming from C++ code.

thanks,
Nat

---------- Forwarded message ----------
From: <[email protected]>
Date: Thu, Jul 22, 2010 at 1:57 PM
Subject: 
To: 


 User name: Elwood Mullins
 E-mail address: [email protected]
 Version: 1.6.3-473
 Platform: mac-intel-osx
 Comments: This error only occurs when I add planarity restraints to the bond and angle restraints in the restraints.edits file.

 Traceback:
RuntimeError : cctbx InternalError: /net/patchnose/scratch1/phenix/phenix-1.6.3-473/cctbx_project/cctbx/geometry_restraints/planarity.h(326): CCTBX_ASSERT(sum_weights > 0) failure.
Traceback:
 File "/usr/local/phenix-1.6.3-473/cctbx_project/libtbx/thread_utils.py", line 141, in run
   return_value = self._target(self._args, self._kwargs, self._c)

 File "/usr/local/phenix-1.6.3-473/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__
   result = self.target()

 File "/usr/local/phenix-1.6.3-473/phenix/phenix/refinement/runtime.py", line 35, in __call__
   call_back_handler=callback)

 File "/usr/local/phenix-1.6.3-473/phenix/phenix/refinement/command_line.py", line 71, in run
   overwrite = command_line_interpreter.command_line.options.overwrite)

 File "/usr/local/phenix-1.6.3-473/phenix/phenix/refinement/driver.py", line 132, in __init__
   assume_hydrogens_all_missing = not has_hd)

 File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3490, in geometry_restraints_manager
   log=self.log)

 File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3243, in construct_geometry_restraints_manager
   params=params_edits, log=log)

 File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3080, in process_geometry_restraints_edits
   sel_cache=sel_cache, params=params, log=log)

 File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3068, in process_geometry_restraints_edits_planarity
   proxy=proxy)



 Platform info:
 __FILE__ = /net/patchnose/scratch1/phenix/phenix-1.6.3-473/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Jul 18 2010
__TIME__ = 03:42:23
__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
PY_VERSION = 2.6.5
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
os.name: posix
sys.platform: darwin
sys.byteorder: little
platform.platform(): Darwin-10.4.0-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 = �










<refinement.geometry_restraints.edits>

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Elwood A. Mullins
Research Associate
Department of Biochemistry
Purdue University
175 South University Street
West Lafayette, IN 47907-1612

Office: Biochemistry 29
Tel: (765) 496-6814
Fax: (765) 494-7897
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

On Jul 21, 2010, at 5:11 PM, Ralf W. Grosse-Kunstleve wrote:

I'm trying to refine a thioester linkage (CoA to
glutamate). Is it possible to define planarity restraints in a
refinement.geometry_restraints.edits file along with bonds and
angles?

Yes, this was added recently by Jeff. In the 1.6.3 release
you can define custom planarities like this:

refinement.geometry_restraints.edits {
 planarity {
   action = *add delete change
   atom_selection = chain A and resid 123 and (name C or name N or name O)
   sigma = 0.02
 }
}

Ralf
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