Hi Nat, fixed in the latest build. Thanks a lot and best wishes Christian Am Donnerstag 08 März 2012 15:14:25 schrieb Nathaniel Echols:

Please update to the latest nightly build (1000!) - I think either Pavel or I fixed this a few weeks ago. (But if not, let us know ASAP.)

-Nat

On Thu, Mar 8, 2012 at 5:37 AM, Christian Roth

wrote:

...

Dear Phenix Team, I started a refinement with anisotropic adp and weight optimization and directly after the optimization step an error appeared which never appeared befor for me. The previous steps of mask optimization and xyz refinement worked well.

Best Regards

Christian

AssertionError : Traceback: File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c)

File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target()

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/runtime.py", line 68, in __call__ call_back_handler=callback)

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/command_line.py", line 97, in run call_back_handler=call_back_handler)

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/driver.py", line 1494, in run ncs_manager = self.ncs_manager)

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/strategies.py", line 1046, in refinement_machine h_params = h_params)

File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 212, in __init__ nproc = nproc)

File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 389, in __init__ compute_gradients=False).target_work())

Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix- dev-979/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 7 2012 __TIME__ = 02:05:24 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 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 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) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 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: 2.10.1 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.31-23-generic-pae-i686-with-debian-squeeze-sid platform.architecture(): ('32bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 25,405,636,608 Memory free: 20,305,633,280 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

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Hi Rajesh, On Mar 9, 2012 10:15 AM, "Rajesh kumar" wrote:

Dear All,

I used "find NCS restraints automatically", " NCS restraints", and NCS

type-torsion angle. Log file has following lines suggesting that it has found NCS and has applied (Am I right?). [ PHENIX (phenix.refine: 1.7.3_928)]

Updating torsion NCS restraints... Number of torsion NCS restraints: 4736

1. PDB file header doesn't have anything written on NCS. I thought PDB

file should have it. Am I missing something? This is a great point. There should probably be NCS output in the PDB header. If you used torsion NCS restraints, a list of matching residues is printed in the .log file.

2. What is difference between NCS type, global and torsion angle, and when they are preferred over the other?

Global NCS uses Cartesian-based restraints, which force the matching chains to be identical. Torsion NCS restraints are new, and restrain matching torsion angles, but are flexible and allow differences between related chains. In general torsion NCS restraints perform better, and are safe to use with even high resolution data where differences between chains can be more pronounced in the map. If you have further questions please let me know. Jeff

Thanks Rajesh

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Hi Jeff,

This is a great point. There should probably be NCS output in the PDB header.

yes, it's definitely good to have, but can we really say more than something like: REMARK 3 NCS RESTRAINTS: TYPE TORSION ?

...

2. What is difference between NCS type, global and torsion angle, and when they are preferred over the other?

Global NCS uses Cartesian-based restraints, which force the matching chains to be identical.

Just a minor correction: what you described are NCS *constraints*, and we don't have them in phenix.refine yet. NCS restraints force the coordinates and B-factors (residual B-factors if TLS is used) of NCS related copies to be *similar* (but not necessarily identical). The degree of similarity is determined by a parameter, and this parameter cannot be set such that NCS restraints become NCS constraints. All the best, Pavel

Hi Rajesh, Thanks for clarifying, I see now what needs to be added to the PDB header. I'll add that functionality for when torsion NCS restraints are used. Jeff On Fri, Mar 9, 2012 at 8:20 PM, Rajesh kumar wrote:

Dear Pavel, With global type, it's written to header but with torsion angle nothing is added to pdb though log file suggests about applying NSC. Except the user nobody will know about the ncs. Thanks Rajesh

Sent from my iPhone

On Mar 9, 2012, at 10:10 PM, "Pavel Afonine" wrote:

...

Hi Jeff,

...

This is a great point. There should probably be NCS output in the PDB header.

yes, it's definitely good to have, but can we really say more than something like:

REMARK 3 NCS RESTRAINTS: TYPE TORSION

?

...

...

2. What is difference between NCS type, global and torsion angle, and when they are preferred over the other?

Global NCS uses Cartesian-based restraints, which force the matching chains to be identical.

Just a minor correction: what you described are NCS *constraints*, and we don't have them in phenix.refine yet. NCS restraints force the coordinates and B-factors (residual B-factors if TLS is used) of NCS related copies to be *similar* (but not necessarily identical). The degree of similarity is determined by a parameter, and this parameter cannot be set such that NCS restraints become NCS constraints.

All the best, Pavel

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---

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Hi Rajesh,

but with torsion angle nothing is added to pdb though log file suggests about applying NSC. Except the user nobody will know about the ncs.

*.geo file contains all the geometry restraints used in refinement, including NCS. So this information is available since any refinement run creates a geo file. Pavel