Re: [phenixbb] Planarity restraint for covalent linkage

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 Email: [email protected] 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 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: [email protected] 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 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 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: [email protected] 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: 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 = Å

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb