[phenixbb] Planarity restraint for covalent linkage

Elwood A. Mullins mullins at purdue.edu
Fri Jul 23 11:16:14 PDT 2010


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: mullins at purdue.edu
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
Email: mullins at purdue.edu
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 <mullins at purdue.edu> 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
> Email: mullins at purdue.edu
> 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 <nechols at lbl.gov> 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 <mullins at purdue.edu> 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
>> Email: mullins at purdue.edu
>> 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: <bugs-from-web at phenix-online.org>
>>> Date: Thu, Jul 22, 2010 at 1:57 PM
>>> Subject: 
>>> To: 
>>> 
>>> 
>>>  User name: Elwood Mullins
>>>  E-mail address: mullins at purdue.edu
>>>  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 = Å
>>> 
>>> 
>>> 
>> 
>> 
>> 
>> 
> 
> 
> 
> <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
Email: mullins at purdue.edu
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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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