[phenixbb] on "Tutorial: Solving a structure with cryo-EM data using docking"

Fri Mar 19 12:48:58 PDT 2021

Hi Smith,

> By clicking "phenix" in my centos 8 terminal, the phenix GUI can be 
> launched, but in the terminal there were messages "Gtk-Message: 
> 11:08:21.204: Failed to load module "pk-gtk-module" and message 
> "Gtk-Message: 11:08:21.205: Failed to load module 
> "canberra-gtk-module". Does this mean I have failed for something for 
> my phenix installation? Which phenix functions it affects? Is any way 
> I install these uninstalled modules at this stage and how to install?

it's just noise. Don't worry about it. Things should work, normally.

> Next, when I run the phenix.real_space_refine as command line in the 
> terminal, it wroks fine. However when I run it in the phenix GUI, I 
> got the following assertion error message (see following between "----").
>
> I am looking forward to getting your reply to have the above issues 
> solved.

We fixed this problem already. Please use the most recent version of 
Phenix located in usual place:

http://phenix-online.org/download/nightly_builds.cgi

Let us know of any other issues!

Pavel

>
> Best wishes,
>
> Smith
>
> ----
>
> AssertionError :
> Traceback:
>   File 
> "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py", 
> line 181, in run
>     return_value = self.target()
>
>   File 
> "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py", 
> line 76, in __call__
>     result = self.run()
>
>   File 
> "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py", 
> line 52, in run
>     self.result.validation_cryoem = self.run_validation()
>
>   File 
> "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py", 
> line 113, in run_validation
>     task.validate()
>
>   File 
> "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/programs/validation_cryoem.py", 
> line 476, in validate
>     self.params.map_model_cc.ignore_symmetry_conflicts)
>
>   File 
> "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py", 
> line 302, in __init__
>     mmmn.shift_origin()
>
>   File 
> "/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py", 
> line 7837, in shift_origin
>     assert approx_equal(existing_shift_cart, expected_model_shift_cart)
>
>
>
> Platform info:
> __FILE__ = 
> /dev/shm/bkpoon/software/release/patch/modules/cctbx_project/boost_adaptbx/meta_ext.cpp
> __DATE__ = Jan 21 2021
> __TIME__ = 11:15:23
> __TIMESTAMP__ = Mon Oct  5 22:43:41 2020
> __x86_64__
> __linux
> __GNUC__ = 4
> __GNUC_MINOR__ = 4
> __GNUC_PATCHLEVEL__ = 7
> __GXX_WEAK__ = 1
> __LP64__ = 1
> __VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-23)
> 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_70
> PY_VERSION = 2.7.15
> PYTHON_API_VERSION = 1013
> sizeof(bool) = 1
> sizeof(short) = 2
> sizeof(int) = 4
> sizeof(long) = 8
> sizeof(std::size_t) = 8
> sizeof(void*) = 8
> 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) = 4
> _OPENMP = 200805
> gnu libc version: 2.28
> BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
> boost/TAG: None
> os.name: posix
> sys.platform: linux2
> sys.byteorder: little
> platform.platform(): 
> Linux-4.18.0-193.28.1.el8_2.x86_64-x86_64-with-centos-8.2.2004-Core
> platform.architecture(): ('64bit', '')
> floating_point_exceptions.division_by_zero_trapped: False
> floating_point_exceptions.invalid_trapped: False
> floating_point_exceptions.overflow_trapped: False
> number of processors: 12
> Memory total:  134,367,047,680
> Memory free:   124,477,964,288
> import thread: OK
> "hello" = ['h', 'e', 'l', 'l', 'o']
> u"hello" = ['h', '\x00', '\x00', '\x00', 'e', '\x00', '\x00', '\x00', 
> 'l', '\x00', '\x00', '\x00', 'l', '\x00', '\x00', '\x00', 'o', '\x00', 
> '\x00', '\x00']
> u"\u00C5" = ['\xc5', '\x00', '\x00', '\x00'] as utf-8 = ['\xc3', '\x85']
> LATIN CAPITAL LETTER A WITH RING ABOVE = Å
>
>
> On Thursday, March 18, 2021, 6:36:32 AM GMT+8, Pavel Afonine 
> <pafonine at lbl.gov> wrote:
>
>
> Hi Smith,
>
> all data files that are used in tutorials are shipped with Phenix. So 
> you don't need to download anything additionally. If you want to use 
> your own data, just do it and follow the tutorial script. In this case 
> your files have the same property as in the tutorial (for example, 
> have symmetry if it is used as part of the tutorial).
>
> Hope this helps!
>
> Pavel
>
> On 3/13/21 18:29, Smith Lee wrote:
> Dear All,
>
> For "Tutorial: Solving a structure with cryo-EM data using docking", 
> it is easy to download the emd_20026_half_map_1_box.ccp4 and 
> emd_20026_half_map_2_box.ccp4 from the emd-20026 depositation, but 
> will you please let me know step by step how to get the tutorial used 
> seq.dat, 20026_auto_sharpen_A.ccp4 (any other name for this file? 
> Cannot find the exact name file  in emd_20026 depositation), 
> apoferritin_chainA_rsr.pdb (it mentioned "model refined against 
> sharpened map", which sharpened map, and what was the refinement 
> method ued?), run_denmod_dock.csh?
>
> I am looking forward to getting your reply.
>
> Best wishes,
>
> Smith
>
>
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