June 2017 - cctbxbb - phenix-online.org

Building cctbx & friends with intel compilers
by Graeme.Winter＠diamond.ac.uk 29 Jun '17

29 Jun '17

Greetings all, Do we have a recipe for compiling cctbx etc with icc? To pick a random example, this version: icc (ICC) 17.0.4 20170411 Copyright (C) 1985-2017 Intel Corporation. All rights reserved. Thanks 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

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incorrect url for downloading fasta files
by R.D. Oeffner 28 Jun '17

28 Jun '17

hi, It would appear that the URL in cctbx_projectiotbxpdbfetch.py for fetching fasta files has been changed by RCSB. So fetch.py therefore downloads garbage when trying to download a fasta file. The correct URL is not documented by RCSB but can be inferred from the RCSB web site when downloading a fasta file. I've updated the URL in fetch.py accordingly. Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

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please read before your next commit
by markus.gerstel＠diamond.ac.uk 27 Jun '17

27 Jun '17

Good morning, recently a couple of large files were erroneously committed to the cctbx repository and then deleted thereafter. Git always keeps a full history, so to avoid cruft aggregating over time we decided to cut those files out of the repository history. Unfortunately this means everyone will have to do a couple of steps: 1. Please ensure you have run libtbx.git_avoid_merges on all of your development machines 2. Run git pull --rebase the next time you update your repository instead of git pull - again, do this on all development machines. 3. If you keep any local branches you may need to rebase them onto master (git fetch; git checkout $branchname; git rebase origin/master) If you don't follow these instructions you may end up recommitting those large files, and we have to start again. Thanks -Markus -- 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

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Housekeeping / roadmap for future
by Graeme.Winter＠diamond.ac.uk 21 Jun '17

21 Jun '17

Hello all, Appreciate a phenix release coming shortly & not suggesting anything any time soon However we were discussing earlier what the road map is for cctbx - making it ready for the future - and I was wondering what is already on the table? Is there a road map somewhere? I recall Billy mentioning Python3 recently, as an example... Thanks 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

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Re: [cctbxbb] bootstrap.py on Windows
by R. D. Oeffner 20 Jun '17

20 Jun '17

Instructions for building on windows are here: https://github.com/cctbx/cctbx_project/wiki Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 -----Original Message----- From: R. D. Oeffner Sent: Tuesday, June 20, 2017 10:37 PM To: horst.puschmann(a)gmail.com ; cctbxbb(a)phenix-online.org Cc: oleg(a)olexsys.org Subject: Re: [cctbxbb] bootstrap.py on Windows Dear Horst, There's a writeup of instructions on how to do CCTBX builds from bootstrap.py on Windows. No authentication is needed for building CCTBX on any platform. Please follow these instructions and get in touch if you have further problems. CCTBX and other projects depending on CCTBX is tested through regression test nightly on LBL machines on all platforms supported. See http://cci-vm-6.lbl.gov:8010/one_line_per_build for log files of these tests. Regards, Robert -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 -----Original Message----- From: markus.gerstel(a)diamond.ac.uk Sent: Tuesday, June 20, 2017 9:25 PM To: horst.puschmann(a)gmail.com ; cctbxbb(a)phenix-online.org Cc: oleg(a)olexsys.org Subject: Re: [cctbxbb] bootstrap.py on Windows Hello Horst, I think the automated tests aren't really covering the bootstrap process. While we extensively test bootstrap at our place, we do not run any tests on Windows. I don't know if LBL runs Windows tests, but if they do they probably run it within buildbot, which means it is not run the same way you run it. Best wishes -Markus ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Horst Puschmann [horst.puschmann(a)gmail.com] Sent: Tuesday, April 04, 2017 09:59 To: cctbxbb(a)phenix-online.org Cc: Oleg Dolomanov (oleg(a)olexsys.org) Subject: [cctbxbb] bootstrap.py on Windows Hello I am trying to install the cctbx on a Windows 7 64 bit machine using the following bootstrap.py file: https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_bu… The script will fail, unless I comment out lines 1101 and 1102: #if self.isPlatformWindows(): #tarurl, arxname, dirpath = MODULES.get_module(module)().get_tarauthenticated(auth=self.get_auth()) If it tries to execute the commented lines, the error will be "KeyError: 'cciuser' in line 590" After commenting this out, it will fail in line 271, with "AttributeError: 'module' object has no attribute '_create_unverified_context'" I can get round that with disabling line 247: if sys.platform == "win32": (i.e. change this to if sys.platform == "xxx":) After that, things start downloading. All appears well until the same thing happens again in another bootstrap.py file in \modules\cctbx_project\libtbx\auto_build\bootstrap.py If I disable *that*, it goes further, but fails finally with ===== Running in build: run configure.py Traceback (most recent call last): File "bootstrap.py", line 2113, in <module> run() File "bootstrap.py", line 2108, in run enable_shared=options.enable_shared, File "bootstrap.py", line 1036, in run i.run() File "bootstrap.py", line 189, in run raise RuntimeError("Could not run %s: File not found" % executable) RuntimeError: Could not run base\bin\python: File not found I guess the automatic tests haven't picked this up, because no authentication is needed, maybe? Greetings Horst -- 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 _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/cctbxbb --- This email has been checked for viruses by AVG. http://www.avg.com

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bootstrap.py on Windows
by Horst Puschmann 20 Jun '17

20 Jun '17

Hello I am trying to install the cctbx on a Windows 7 64 bit machine using the following bootstrap.py file: https://raw.githubusercontent.com/cctbx/cctbx_project/ master/libtbx/auto_build/bootstrap.py The script will fail, unless I comment out lines 1101 and 1102: #if self.isPlatformWindows(): #tarurl, arxname, dirpath = MODULES.get_module(module)().get_tarauthenticated(auth=self.get_auth()) If it tries to execute the commented lines, the error will be "KeyError: 'cciuser' in line 590" After commenting this out, it will fail in line 271, with "AttributeError: 'module' object has no attribute '_create_unverified_context'" I can get round that with disabling line 247: if sys.platform == "win32": (i.e. change this to if sys.platform == "xxx":) After that, things start downloading. All appears well until the same thing happens again in another bootstrap.py file in \modules\cctbx_project\libtbx\auto_build\bootstrap.py If I disable *that*, it goes further, but fails finally with ===== Running in build: run configure.py Traceback (most recent call last): File "bootstrap.py", line 2113, in <module> run() File "bootstrap.py", line 2108, in run enable_shared=options.enable_shared, File "bootstrap.py", line 1036, in run i.run() File "bootstrap.py", line 189, in run raise RuntimeError("Could not run %s: File not found" % executable) RuntimeError: Could not run base\bin\python: File not found I guess the automatic tests haven't picked this up, because no authentication is needed, maybe? Greetings Horst

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bioinformatics.SE
by Marcin Wojdyr 16 Jun '17

16 Jun '17

Hello, just to let you know, a few weeks ago StackExchange started a Bioinformatics Q&A site. Like Biostars, it's mostly about sequences, but sometimes people pop up with questions that could be answered using cctbx, for example a few minutes ago: https://bioinformatics.stackexchange.com/questions/783/how-can-we-find-the-…

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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

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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

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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

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