- cctbxbb - phenix-online.org

Fwd: [git/cctbx] master: Making cif behavior exactly the same as pdb (throwing away SCALE records if crystal_symmetry is supplied to obtain xray_structure). With test. (bdf35cf1c)
by Graeme.Winter＠diamond.ac.uk 16 Jun '17

16 Jun '17

Please could people refrain from making cctbx tests dependent on phenix tools? E.g. not easy_run.call("phenix.cif_as_pdb %s.cif > junk.out"%prefix) Obliged in anticipation Cheers Graeme Begin forwarded message: From: CCTBX Commit via DLS Jenkins <graeme.winter(a)GMAIL.COM<mailto:[email protected]>> Subject: [git/cctbx] master: Making cif behavior exactly the same as pdb (throwing away SCALE records if crystal_symmetry is supplied to obtain xray_structure). With test. (bdf35cf1c) Date: 15 June 2017 at 19:43:57 BST To: <CCTBX-COMMIT(a)JISCMAIL.AC.UK<mailto:[email protected]>> Reply-To: <cctbxbb(a)PHENIX-ONLINE.ORG<mailto:[email protected]>> Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx On branch : master ________________________________ commit bdf35cf1c69d235d2578d915836aad2a739c1c15 Author: Oleg Sobolev <osobolev(a)lbl.gov<mailto:[email protected]>> Date: Thu Jun 15 11:43:52 2017 -0700 Making cif behavior exactly the same as pdb (throwing away SCALE records if crystal_symmetry is supplied to obtain xray_structure). With test. ________________________________ bdf35cf1c69d235d2578d915836aad2a739c1c15 iotbx/pdb/mmcif.py | 24 +++++----- iotbx/regression/tst_xray_scale.py | 93 ++++++++++++++++++++++++++++++++++++++ iotbx/run_tests.py | 1 + 3 files changed, 107 insertions(+), 11 deletions(-) diff --git a/iotbx/pdb/mmcif.py b/iotbx/pdb/mmcif.py index 6a5221a6a..2b79df99a 100644 --- a/iotbx/pdb/mmcif.py +++ b/iotbx/pdb/mmcif.py @@ -508,17 +508,19 @@ class cif_input(iotbx.pdb.pdb_input_mixin): return extract_tls_from_cif_block(self.cif_block, hierarchy) def scale_matrix(self): - fractionalization_matrix = [ - self.cif_block.get('_atom_sites.fract_transf_matrix[%s][%s]' %(i, j)) - for i,j in ('11', '12', '13', '21', '22', '23', '31','32', '33')] - if fractionalization_matrix.count(None) == 9: - return None - assert fractionalization_matrix.count(None) == 0 - fractionalization_vector = [ - self.cif_block.get('_atom_sites.fract_transf_vector[%s]' %i) for i in '123'] - assert fractionalization_matrix.count(None) == 0 - return [[float(i) for i in fractionalization_matrix], - [float(i) for i in fractionalization_vector]] + if (not hasattr(self, "_scale_matrix")): + fractionalization_matrix = [ + self.cif_block.get('_atom_sites.fract_transf_matrix[%s][%s]' %(i, j)) + for i,j in ('11', '12', '13', '21', '22', '23', '31','32', '33')] + if fractionalization_matrix.count(None) == 9: + return None + assert fractionalization_matrix.count(None) == 0 + fractionalization_vector = [ + self.cif_block.get('_atom_sites.fract_transf_vector[%s]' %i) for i in '123'] + assert fractionalization_matrix.count(None) == 0 + self._scale_matrix = [[float(i) for i in fractionalization_matrix], + [float(i) for i in fractionalization_vector]] + return self._scale_matrix def model_ids(self): return flex.std_string([model.id for model in self.hierarchy.models()]) diff --git a/iotbx/regression/tst_xray_scale.py b/iotbx/regression/tst_xray_scale.py new file mode 100644 index 000000000..e1a4ec9f3 --- /dev/null +++ b/iotbx/regression/tst_xray_scale.py @@ -0,0 +1,93 @@ +from __future__ import division +from libtbx import easy_run +import iotbx.pdb +from cctbx import crystal +from libtbx.test_utils import approx_equal + +cif_str=""" +data_5JUP +# +_atom_sites.entry_id 5JUP +_atom_sites.fract_transf_matrix[1][1] 1.000000 +_atom_sites.fract_transf_matrix[1][2] 0.000000 +_atom_sites.fract_transf_matrix[1][3] 0.000000 +_atom_sites.fract_transf_matrix[2][1] 0.000000 +_atom_sites.fract_transf_matrix[2][2] 1.000000 +_atom_sites.fract_transf_matrix[2][3] 0.000000 +_atom_sites.fract_transf_matrix[3][1] 0.000000 +_atom_sites.fract_transf_matrix[3][2] 0.000000 +_atom_sites.fract_transf_matrix[3][3] 1.000000 +_atom_sites.fract_transf_vector[1] 0.00000 +_atom_sites.fract_transf_vector[2] 0.00000 +_atom_sites.fract_transf_vector[3] 0.00000 +# +loop_ +_atom_type.symbol +C +MG +N +O +P +S +# +loop_ +_atom_site.group_PDB +_atom_site.id +_atom_site.type_symbol +_atom_site.label_atom_id +_atom_site.label_alt_id +_atom_site.label_comp_id +_atom_site.label_asym_id +_atom_site.label_entity_id +_atom_site.label_seq_id +_atom_site.pdbx_PDB_ins_code +_atom_site.Cartn_x +_atom_site.Cartn_y +_atom_site.Cartn_z +_atom_site.occupancy +_atom_site.B_iso_or_equiv +_atom_site.auth_seq_id +_atom_site.auth_comp_id +_atom_site.auth_asym_id +_atom_site.auth_atom_id +_atom_site.pdbx_PDB_model_num +ATOM 9 C "C3'" . U A 1 1 ? 175.229 258.091 229.127 1.00 113.67 1 U A "C3'" 1 +ATOM 7 C "C4'" . U A 1 1 ? 175.388 257.913 227.616 1.00 113.21 1 U A "C4'" 1 +ATOM 6 C "C5'" . U A 1 1 ? 174.124 257.916 226.769 1.00 114.11 1 U A "C5'" 1 +ATOM 10 O "O3'" . U A 1 1 ? 176.253 257.344 229.761 1.00 112.89 1 U A "O3'" 1 +ATOM 8 O "O4'" . U A 1 1 ? 176.291 258.974 227.185 1.00 112.70 1 U A "O4'" 1 +ATOM 5 O "O5'" . U A 1 1 ? 173.735 259.270 226.430 1.00 115.09 1 U A "O5'" 1 +ATOM 3 O OP1 . U A 1 1 ? 174.056 259.302 223.918 1.00 117.16 1 U A OP1 1 +ATOM 4 O OP2 . U A 1 1 ? 172.661 261.090 225.058 1.00 104.87 1 U A OP2 1 +ATOM 1 O OP3 . U A 1 1 ? 171.796 258.709 224.899 1.00 116.23 1 U A OP3 1 +ATOM 2 P P . U A 1 1 ? 173.022 259.610 224.994 1.00 116.34 1 U A P 1 +# +""" + +def run(prefix="iotbx_tst_xray_scale"): + """ + Exercise obtaining exactly the same xray structure from pdb and cif. + Caveate is SCALE records (fract_transf_matrix). In pdb they explicitly + suppressed when crystal_symmetry is supplied, see + iotbx/pdb/__init__.py:939 (def xray_structure_simple): + if(crystal_symmetry is not None): self._scale_matrix = None + """ + fo = open("%s.cif" % prefix,"w") + print >> fo, cif_str + fo.close() + # crystal symmetry from map + cs = crystal.symmetry((419., 419., 419., 90.0, 90.0, 90.0), 1) + # xrs from mmCIF + cif_inp = iotbx.pdb.input(file_name="%s.cif" % prefix) + # print "======== doing xrs from cif ==============" + xrs_cif = cif_inp.xray_structure_simple(crystal_symmetry = cs) + # xrs from PDB + easy_run.call("phenix.cif_as_pdb %s.cif > junk.out"%prefix) + pdb_inp = iotbx.pdb.input(file_name="%s.pdb" % prefix) + # print "======== doing xrs from pdb ==============" + xrs_pdb = pdb_inp.xray_structure_simple(crystal_symmetry = cs) + # + assert approx_equal(xrs_cif.sites_cart()[0], xrs_pdb.sites_cart()[0]) + +if (__name__ == "__main__"): + run() diff --git a/iotbx/run_tests.py b/iotbx/run_tests.py index 52eb3d2e4..9f3e50a98 100644 --- a/iotbx/run_tests.py +++ b/iotbx/run_tests.py @@ -93,6 +93,7 @@ tst_list = ( "$D/regression/tst_show_systematic_absences.py", "$D/regression/tst_miller_sort_asu.py", "$D/regression/tst_reflection_file_reader.py", + "$D/regression/tst_xray_scale.py", ) def run(): -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

1 1

Backwards compatibility; Python 2.3?
by Nicholas Devenish 12 Jun '17

12 Jun '17

Hi All, I'm starting to go through and learn some of the structure of these packages, starting with libtbx. What's the supported targets supposed to be? There seems to be code specifically marked as backwards compatibility for Python 2.3 (2003), and packages explicitly included that were merged into the standard library around the same time (e.g. Optik). Is this really as far back as we need to support? Thanks, Nick Devenish

7 12

bz2 support on Ubuntu
by David Waterman 08 Jun '17

08 Jun '17

Hi folks, My bootstrap build of cctbx/DIALS on Ubuntu 16.04.2 LTS produces a base Python that does not have bz2 support. This is despite the fact that the package "libbz2-dev is already the newest version (1.0.6-8)." Looking in Python_install_log I see Python build finished, but the necessary bits to build these modules were not found: _bsddb _curses _curses_panel _sqlite3 _tkinter bsddb185 bz2 dbm dl gdbm imageop readline sunaudiodev Has anyone got any ideas? Anyone done a boostrap build on Ubuntu where bz2 can be imported in Python? Also, what's the procedure to rebuild from base, recovering all the currently configured modules? My guess is that something like this would do it, but is there a better way? export MYMODULES=$(libtbx.list_modules | tr '\n' ' ') rm -rf base_tmp/ base/ build/ python bootstrap.py --builder=dials base python bootstrap.py --builder=dials build cd build source setpaths.sh libtbx.configure $MYMODULES make Cheers -- David

2 3

simtbx
by Graeme.Winter＠diamond.ac.uk 05 Jun '17

05 Jun '17

Hi Folks We have noticed that simtbx, part of the core cctbx now, depends on dials This means if you do not have a dials build your cctbx will be broken This is probably not the way we want things? I thought simtbx was a separate repo? Cheerio Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

7 17

cctbx has acquired a hidden dependency on iotbx
by Luc Bourhis 27 May '17

27 May '17

Hi, C:\Users\luc\Documents\Developer\cctbx\modules\cctbx_project\cctbx\maptbx\SConscript, line 5-8: env = env_base.Clone( SHLINKFLAGS=env_etc.shlinkflags, LIBS=["iotbx_xplor", "cctbx_sgtbx_asu", "cctbx", "omptbx", env_etc.libm] ) This is not supposed to be: the cctbx shall be usable with only what’s defined in its libtbx_config. Best wishes, Luc

3 2

shall iotbx really depends on dxtbx?
by Luc Bourhis 26 May '17

26 May '17

Hi, iotbx/libtbx_config: { "modules_required_for_use": ["cctbx", "fable", "ucif", "smtbx", "dxtbx"], "optional_modules": ["ccp4io", "cbflib"], } A search for dxtbx in the source code of iotbx does not return anything. Did I miss something? Moreover dxtbx/libtbx_config: { "modules_required_for_use" : [ "iotbx" ], } The problem is that dxtbx pulls in HDF5 and that it fails to compiles on Windows 64 with a 64-bit Python, a configuration we need for Olex 2. If the solution was as simple as dropping the dependence of iotbx on dxtbx, that would make my day! Thoughts? Best wishes, Luc Bourhis

3 4

probe/reduce repositories
by Hattne, Johan 04 May '17

04 May '17

Dear all; I appear to be missing probe in my source build. On running phenix.model_vs_data I get the traceback posted below. The error message appears to be a tad misleading, because having probe in PATH is not enough: the actual test in the code is if (not libtbx.env.has_module(name="probe")): which leads me to believe that I’m supposed to have something probe-like in my source tree, but the duke-server I used to get these kinds of things from (quidditch?) seems unresponsive from here. This is the first time in weeks that I’m doing this, so it is very much likely that whatever happened to break my setup happened quite some time ago. Cluebat, anyone? // Cheers; Johan Traceback (most recent call last): File "/mnt/gonen/home/hattnej/projects/phenix-build/../phenix-src/phenix/phenix/command_line/model_vs_data.py", line 6, in <module> show_geometry_statistics = True) File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_project/mmtbx/model_vs_data.py", line 710, in run atom_selections = atom_selections) File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_project/mmtbx/model_vs_data.py", line 346, in show_geometry restraints_manager = restraints_manager) File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_project/mmtbx/model_statistics.py", line 138, in __init__ molprobity_scores=molprobity_scores) File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_project/mmtbx/model_statistics.py", line 51, in __init__ self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore() File "/mnt/gonen/home/hattnej/projects/phenix-src/cctbx_project/mmtbx/validation/clashscore.py", line 90, in __init__ "http://kinemage.biochem.duke.edu/") RuntimeError: Probe could not be detected on your system. Please make sure Probe is in your path. Probe is available at http://kinemage.biochem.duke.edu/ Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

2 5

normalize() is not safe
by Oleg Sobolev 02 May '17

02 May '17

Dear colleagues, I recently discovered that normalize() function of scitbx::vec3<double> is not safe, i.e. this case scitbx::vec3<double> a(0,0,0); a.normalize(); it will produce division by zero and fail. If function contains this being called from python the traceback would be rather vague: <...> Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. The code that generates this error sits in scitbx/vec3.h, lines 143-153 with a comment that this was done intentionally and a pointer to an appropriate function to do safe normalization. This function is not wrapped to be available in python directly. Similar functionality (but coded in a different place) accessible via python by: >>> from scitbx import matrix >>> b = matrix.col([0,0,0]) >>> b.normalize() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 270, in normalize return self / abs(self) File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 158, in __truediv__ return rec([e/other for e in self.elems], self.n) ZeroDivisionError: float division by zero Fast grepping shows that normalize() is widely used in xfel, smtbx, rstbx, dxtbx, mmtbx/hydrogens, scitbx/rigid_body, and in some other places. My questions to CCTBX community are: 1. Were you aware of this issue? 2. Should we do something about it: - make the function more safe and slow; - leave it like it is and let everybody know about the issue and let developers deal with it individually; 3. Any other input on the matter? Best regards, Oleg Sobolev.

5 5

Boost Python 1.56
by Luc Bourhis 14 Apr '17

14 Apr '17

Hi, I have improvements to the smtbx on their way to be committed which require Boost version 1.56. This is related to Boost.Threads, whose support I re-activated a few months ago on Nick’s request. I need the function boost::thread::physical_concurrency which returns the number of physical cores on the machine, as opposed to virtual cores when hyperthreading is enabled (which it is by default on any Intel machine). That function is not available in Boost 1.55 which is the version currently used in the nightly tests: it appeared in 1.56. So, would it be possible to move to Boost 1.56? Otherwise, I will need to backport that function. Not too difficult but not thrilling. Best wishes, Luc

14 36

Re: [cctbxbb] [git/cctbx] master: Replacing illegal C++ code with proper dynamic array allocation. (a31eb2bf0)
by Nicholas Sauter 12 Apr '17

12 Apr '17

Rob, Just as a general thing, "new" statements in C++ need to be paired with "delete" statements (delete pk, delete a_sum, and delete akml). Unless this is done there will be a memory leak. Nick Nicholas K. Sauter, Ph. D. Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Tue, Apr 11, 2017 at 3:31 AM, CCTBX Commit via DLS Jenkins < graeme.winter(a)gmail.com> wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------ > > > commit a31eb2bf0d5bb129425bb759466f45622c773fd4 > Author: Robert Oeffner <rdo20(a)cam.ac.uk> > Date: Tue Apr 11 11:31:24 2017 +0100 > > Replacing illegal C++ code with proper dynamic array allocation. > > > ------------------------------ > > > a31eb2bf0d5bb129425bb759466f45622c773fd4 > scitbx/lbfgs.h | 6 +++--- > 1 file changed, 3 insertions(+), 3 deletions(-) > > diff --git a/scitbx/lbfgs.h b/scitbx/lbfgs.h > index 41be8e8cc..f0000143d 100755 > --- a/scitbx/lbfgs.h > +++ b/scitbx/lbfgs.h > @@ -917,9 +917,9 @@ namespace lbfgs { > int info = 5; > brackt = false; > FloatType sxnorm = std::sqrt(ddot(SizeType(n), sx, sx)); > - FloatType pk[n]; > - FloatType a_sum[n]; > - FloatType akm1[n]; > + FloatType* pk = new FloatType[n]; > + FloatType* a_sum = new FloatType[n]; > + FloatType* akm1 = new FloatType[n]; > for (SizeType i=0; i < n; i++) { > pk[i] = sx[i]/sxnorm; > akm1[i] = -gx[i]/sxnorm; >

3 2