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<div dir="ltr" data-setdir="false"><div dir="ltr" data-setdir="false"><div>Dear All,</div><div dir="ltr"><br clear="none"></div><div dir="ltr"><span>By clicking "phenix" in my centos 8 terminal, the phenix GUI can be launched, but in the terminal there were messages "<span>Gtk-Message: 11:08:21.204: Failed to load module "pk-gtk-module" and message "<span>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?</span></span></span></div><div dir="ltr"><span><span><span><br clear="none"></span></span></span></div><div dir="ltr"><span><span><span>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 "----").</span></span></span></div><div dir="ltr"><span><span><span><br clear="none"></span></span></span></div><div dir="ltr"><span><span><span>I am looking forward to getting your reply to have the above issues solved.</span></span></span></div><div dir="ltr"><span><span><span><br clear="none"></span></span></span></div><div dir="ltr"><span><span><span>Best wishes,</span></span></span></div><div dir="ltr"><span><span><span><br clear="none"></span></span></span></div><div dir="ltr"><span><span><span>Smith</span></span></span></div><div dir="ltr"><span><span><span><br clear="none"></span></span></span></div><div dir="ltr"><span><span><span>----</span></span></span></div><span><span></span></span><br clear="none">AssertionError : <br clear="none">Traceback:<br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py",
line 181, in run<br clear="none"> return_value = self.target()<br clear="none"><br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/libtbx/runtime_utils.py",
line 76, in __call__<br clear="none"> result = self.run()<br clear="none"><br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py",
line 52, in run<br clear="none"> self.result.validation_cryoem = self.run_validation()<br clear="none"><br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/wxGUI2/program_template/real_space_refine.py",
line 113, in run_validation<br clear="none"> task.validate()<br clear="none"><br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/phenix/phenix/programs/validation_cryoem.py",
line 476, in validate<br clear="none"> self.params.map_model_cc.ignore_symmetry_conflicts)<br clear="none"><br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py",
line 302, in __init__<br clear="none"> mmmn.shift_origin()<br clear="none"><br clear="none">
File
"/home/myphenix/phenix11914122installdir/phenix-1.19.1-4122/modules/cctbx_project/iotbx/map_model_manager.py",
line 7837, in shift_origin<br clear="none"> assert approx_equal(existing_shift_cart, expected_model_shift_cart)<br clear="none"><br clear="none"><br clear="none"><br clear="none">Platform info:<br clear="none">__FILE__ = /dev/shm/bkpoon/software/release/patch/modules/cctbx_project/boost_adaptbx/meta_ext.cpp<br clear="none">__DATE__ = Jan 21 2021<br clear="none">__TIME__ = 11:15:23<br clear="none">__TIMESTAMP__ = Mon Oct 5 22:43:41 2020<br clear="none">__x86_64__<br clear="none">__linux<br clear="none">__GNUC__ = 4<br clear="none">__GNUC_MINOR__ = 4<br clear="none">__GNUC_PATCHLEVEL__ = 7<br clear="none">__GXX_WEAK__ = 1<br clear="none">__LP64__ = 1<br clear="none">__VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-23)<br clear="none">FE_INEXACT = 32<br clear="none">FE_DIVBYZERO = 4<br clear="none">FE_UNDERFLOW = 16<br clear="none">FE_OVERFLOW = 8<br clear="none">FE_INVALID = 1<br clear="none">FE_ALL_EXCEPT = 61<br clear="none">__SSE2__ = 1<br clear="none">BOOST_LIB_VERSION = 1_70<br clear="none">PY_VERSION = 2.7.15<br clear="none">PYTHON_API_VERSION = 1013<br clear="none">sizeof(bool) = 1<br clear="none">sizeof(short) = 2<br clear="none">sizeof(int) = 4<br clear="none">sizeof(long) = 8<br clear="none">sizeof(std::size_t) = 8<br clear="none">sizeof(void*) = 8<br clear="none">sizeof(long long) = 8<br clear="none">sizeof(float) = 4<br clear="none">sizeof(double) = 8<br clear="none">sizeof(long double) = 16<br clear="none">sizeof(boost::int32_t) = 4<br clear="none">sizeof(boost::uint32_t) = 4<br clear="none">sizeof(wchar_t) = 4<br clear="none">__PTRDIFF_TYPE__<br clear="none">Py_USING_UNICODE<br clear="none">sizeof(PY_UNICODE_TYPE) = 4<br clear="none">_OPENMP = 200805<br clear="none">gnu libc version: 2.28<br clear="none">BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG<br clear="none">boost/TAG: None<br clear="none">os.name: posix<br clear="none">sys.platform: linux2<br clear="none">sys.byteorder: little<br clear="none">platform.platform(): Linux-4.18.0-193.28.1.el8_2.x86_64-x86_64-with-centos-8.2.2004-Core<br clear="none">platform.architecture(): ('64bit', '')<br clear="none">floating_point_exceptions.division_by_zero_trapped: False<br clear="none">floating_point_exceptions.invalid_trapped: False<br clear="none">floating_point_exceptions.overflow_trapped: False<br clear="none">number of processors: 12<br clear="none">Memory total: 134,367,047,680<br clear="none">Memory free: 124,477,964,288<br clear="none">import thread: OK<br clear="none">"hello" = ['h', 'e', 'l', 'l', 'o']<br clear="none">u"hello"
= ['h', '\x00', '\x00', '\x00', 'e', '\x00', '\x00', '\x00', 'l',
'\x00', '\x00', '\x00', 'l', '\x00', '\x00', '\x00', 'o', '\x00',
'\x00', '\x00']<br clear="none">u"\u00C5" = ['\xc5', '\x00', '\x00', '\x00'] as utf-8 = ['\xc3', '\x85']<br clear="none">LATIN CAPITAL LETTER A WITH RING ABOVE = Å<br clear="none"></div><div><br></div></div><div><br></div>
</div><div id="yahoo_quoted_6877009528" class="yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
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On Thursday, March 18, 2021, 6:36:32 AM GMT+8, Pavel Afonine <pafonine@lbl.gov> wrote:
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<div><div id="yiv3918597431"><div>
<p>Hi Smith,</p>
<p>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).</p>
<p>Hope this helps!</p>
<p>Pavel<br clear="none">
</p>
<div class="yiv3918597431yqt1414037113" id="yiv3918597431yqt74033"><div class="yiv3918597431moz-cite-prefix">On 3/13/21 18:29, Smith Lee wrote:<br clear="none">
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<blockquote type="cite">
</blockquote></div></div><div class="yiv3918597431yqt1414037113" id="yiv3918597431yqt53980"><div><div class="yiv3918597431yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;">
<div dir="ltr">Dear All,</div>
<div dir="ltr"><br clear="none">
</div>
<div dir="ltr">
<div dir="ltr">For "<span>Tutorial:
Solving a structure with cryo-EM data using docking", it
is easy to download the <span>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 <span>seq.dat, <span>20026_auto_sharpen_A.ccp4
(any other name for this file? Cannot find the exact
name file in emd_20026 <span><span><span>depositation</span></span></span>),
<span>apoferritin_chainA_rsr.pdb (it mentioned "<span>model
refined against sharpened map", which sharpened
map, and what was the refinement method ued?</span>),
</span></span></span></span></span><span></span><span>run_denmod_dock.csh?</span></div>
<div dir="ltr"><span><br clear="none">
</span></div>
<div dir="ltr"><span>I am looking forward
to getting your reply.</span></div>
<div dir="ltr"><span><br clear="none">
</span></div>
<div dir="ltr"><span>Best wishes,</span></div>
<div dir="ltr"><span><br clear="none">
</span></div>
<div dir="ltr"><span>Smith<br clear="none">
</span></div>
<div dir="ltr"><span></span><br clear="none">
</div>
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