- cctbxbb - phenix-online.org

cctbx.miller problem
by 李选选 06 Dec '17

06 Dec '17

> > Dear cctbx developers, > > I’m Xuanxuan, and I’m using cctbx to develop a crystallography-related algorithm. Recently, I found there is something wrong when I use miller package to generate miller indices for given space group and unit cell parameters. Maybe it’s my mistake, or it’s a bug. > > Here are some details. I just use the following code to generate a list of miller indices for a Fd-3m crystal. > > ms = miller.build_set( > crystal_symmetry=crystal.symmetry( > space_group_symbol='Fd-3m', > unit_cell=(5.4307,5.4307,5.4307,90.00,90.0,90.00)), > anomalous_flag=False, > d_min=0.4) > > And I found some reflections are missing, like 220, 311, which should exist according to the reflection conditions listed in this page http://img.chem.ucl.ac.uk/sgp/large/227az2.htm <http://img.chem.ucl.ac.uk/sgp/large/227az2.htm>. > > Looking forward to your response. > > Thanks, > Xuanxuan

5 4

rotate_translate_map function causes "splinching"
by Pearce, N.M. (Nick) 29 Nov '17

29 Nov '17

Hi all, I’m having a problem with the rotate_translate_map function from cctbx.maptbx. I have a 3D array (a mask of 0s and 1s, in this case) that I’m writing as a CCP4 map file. If I write it out “on the origin” (without running rotate_translate_map), then it’s fine (see attached “before.png”). However, if I apply the rotate_translate_map function and then write it out, odd features appear at the edge of the unit cell (see “after.png”). It is NOT the case that the map is going through the “periodic boundary conditions” of the unit cell (the shift is less than one unit cell, as shown by the structure which is transformed by the same amount). The minimal code is: ——————————— array = cctbx.maptbx.rotate_translate_map( unit_cell=self.unit_cell(), map_data=array, rotation_matrix=scitbx.matrix.rec([1,0,0,0,1,0,0,0,1], (3,3)).elems, translation_vector=(-1.0*scitbx.matrix.rec((X,Y,Z), (3,1))).elems ) # Write the map iotbx.ccp4_map.write_ccp4_map( file_name=f_name, unit_cell=self.unit_cell(), space_group=self.space_group(), map_data=array, labels=flex.std_string(['’]) ) ——————————— where (X,Y,Z) is a tuple for the origin shift. Is there something stupid that I’m missing? Has anyone else had the same problem? The only code for a rotate_translate_map function I could find was actually in maptbx/average_densities.h and I couldn’t see anything obviously “wrong”… though I’m not that familiar with C++. The maps and files can be found at https://www.dropbox.com/sh/xqrsk5lcn603416/AABiVO74g6A_jZMGn_DjxOmka?dl=0 all “grid” files are without translation, and all “ref” files are after translation. both are written out exactly the same (the iotbx.ccp4_map call above). I’m using the cctbx bundled with a ccp4 nightly from 2016-10-22. Thanks, Nick [cid:[email protected]][cid:[email protected]]

2 1

cctbx versions causing indentation crash?
by Magnus Andersson 10 Nov '17

10 Nov '17

Hi all, I have a script that runs fine on my old computer, but crashes on my new computer with the error message: IndentationError: unexpected indent This script is (amongst other things) calling the softwatre Coot such as: subprocess.call(["""coot --no-graphics<<end/n (handle-read-draw-molecule-with-recentre \""""+str(inf)+"""\" 1) (set-refinement-immediate-replacement 1) (set-refine-max-residues 40) (regularize-zone 0 \" \" """+str(res1-2)+""" """+str(res3)+"""\" \") (accept-regularizement) (regularize-zone 0 \" \" """+str(res3)+""" """+str(res2+2)+"""\" \") (accept-regularizement) (write-pdb-file 0 \""""+str(outf)+"""\") (coot-real-exit 0)"""], shell=True) which is ok on my old system. I am trying to find the most likely source of this error. Here are the differences: - OLD cctbx = uses Python 2.7.10, NEW cctbx 2.7.14 - OLD OSX = 10.10.5 (i.e. Yosemite), NEW OSX = 10.11.5 (i.e. El Capitan) - OLD Coot = vers 0.8, NEW Coot = vers 0.8.8 [old Coot install was from Fink but this shouldn’t matter I think] Perhaps someone has encountered something similar or has an educated guess on whether different cctbx versions can cause such errors? Thanks, Magnus #### Magnus Andersson, Docent, Ph.D. Email: magnus.andersson(a)scilifelab.se Phone: 0769469872 Mailing address: Science For Life Laboratory Alpha 6 Box 1031 171 21 Solna Visiting address: Tomtebodavägen 23A 171 65 Solna

2 2

scipy module
by Magnus Andersson 06 Nov '17

06 Nov '17

Hello, I am not normally using cctbx but I’m trying to run a script that imports modules as follows: import sys,io,os import subprocess import numpy import pickle import math import pylab #import pymol import time import scipy import iotbx.pdb import cctbx import mmtbx.model from scipy.optimize import fmin, fmin_cg, leastsq from scipy.interpolate import interp1d import datetime from numpy.random import random_sample from cctbx.array_family import flex from scitbx.math import superpose I have installed cctbx and run with cctbx.python. How can I import scipy into the cctbx python? Cheers, Magnus #### Magnus Andersson, Docent, Ph.D. Email: magnus.andersson(a)scilifelab.se Phone: 0769469872 Mailing address: Science For Life Laboratory Alpha 6 Box 1031 171 21 Solna Visiting address: Tomtebodavägen 23A 171 65 Solna

3 3

Re: [cctbxbb] [git/cctbx] master: libtbx.clean_clutter runs isort in supported locations (612869130)
by Aaron Brewster 26 Oct '17

26 Oct '17

Hi Markus, could isort be added as a dependency instead? If I understand this commit right, when running libtbx.clean_clutter, if .isort.cfg is present and isort is not installed, pip is invoked to install isort. l'm nervous about pip being imported anywhere in our code, especially to install things when running code unrelated to installation. It's important to keep installation of stuff separate from running of stuff. Otherwise, it's impossible to keep dependencies straight. -Aaron On Thu, Oct 26, 2017 at 2:29 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 612869130a6210d49a573a3cff04416a9de67808 > Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk> > Date: Thu Oct 26 10:29:05 2017 +0100 > > libtbx.clean_clutter runs isort in supported locations > > > ------------------------------ > > > 612869130a6210d49a573a3cff04416a9de67808 > libtbx/command_line/clean_clutter.py | 26 ++++++++++++++++++++++++++ > 1 file changed, 26 insertions(+) > > diff --git a/libtbx/command_line/clean_clutter.py > b/libtbx/command_line/clean_clutter.py > index d49bf4c25..8fc2e53c8 100644 > --- a/libtbx/command_line/clean_clutter.py > +++ b/libtbx/command_line/clean_clutter.py > @@ -32,6 +32,24 @@ def clean_clutter_in(files, tabsize=8): > os.remove(tmpname) > raise > > +def isort(path): > + try: > + import mock > + from isort.main import main > + except ImportError: > + # Install package if necessary > + import pip > + pip.main(['install', 'isort', 'mock']) > + import mock > + from isort.main import main > + with mock.patch.object(sys, 'argv', ['isort', '-y', '-ac', '-vb']): > + oldcwd = os.getcwd() > + try: > + os.chdir(path) > + main() > + finally: > + os.chdir(oldcwd) > + > def run(): > opt_parser = (option_parser( > usage=""" > @@ -60,6 +78,7 @@ by running svn commit.""") > if co.committing and files: > opt_parser.show_help() > exit(1) > + run_isort_in_path = False > if co.committing: > try: > files = list(subversion.marked_for_commit()) > @@ -72,7 +91,14 @@ by running svn commit.""") > else: dir = files[0] > files = [ c.path for c in libtbx.file_clutter.gather([dir]) > if c.is_cluttered(flag_x=False) ] > + if os.path.exists(os.path.join(dir, '.isort.cfg')): > + run_isort_in_path = dir > clean_clutter_in(files, tabsize=co.tabsize) > + if run_isort_in_path: > + try: > + isort(run_isort_in_path) > + except Exception as e: > + print("Did not run isort (%s)" % str(e)) > > if (__name__ == "__main__"): > import sys >

2 2

Re: [cctbxbb] Scons for python3 released
by markus.gerstel＠diamond.ac.uk 20 Oct '17

20 Oct '17

That's 3 weeks from now. If we do a 3 week freeze for every DIALS release, plus for phenix releases etc, cctbx would be trapped in perma-frost :) Feel free to start on it now - if it causes issues I can always pick a stable point in the past to branch off from. -Markus On 10 Oct 2017 6:34 pm, Billy Poon <bkpoon(a)lbl.gov> wrote: Great! There's a DIALS release on October 31, so I can start making changes after that. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Tue, Oct 10, 2017 at 1:54 AM, R. D. Oeffner <rdo20(a)cam.ac.uk<mailto:[email protected]>> wrote: http://scons.org/scons-300-is-available.html Perhaps start using this to easy upgrading cctbx to python 3 -- 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<http://www.cimr.cam.ac.uk/investigators/read/index.html> tel: +44(0)1223 763234 _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb -- 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

5 6

Update to allsvn script?
by Graeme.Winter＠diamond.ac.uk 20 Oct '17

20 Oct '17

Folks, phenix_regression/allsvn assumes if you are using git that you are using git/svn These days probably not true ;o) Viz: cd cctbx_project; git svn rebase Unable to determine upstream SVN information from working tree history ccp4io: At revision 160. ccp4io_adaptbx: At revision 142. cd dials; git svn rebase Unable to determine upstream SVN information from working tree history someone on phenix-land want to have a look at this? Obviously not a blocker but is untidy! 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

2 2

Re: [cctbxbb] [git/cctbx] master: Add --print_statement checking capability to libtbx.find_clutter (d499b973b)
by Aaron Brewster 19 Oct '17

19 Oct '17

Hi, should this have been from __future__ import print_function ? Thanks, -Aaron On Thu, Oct 19, 2017 at 1:33 PM, 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 d499b973be4c0443e607fbad13e495bb450938a3 > Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk> > Date: Thu Oct 19 21:33:54 2017 +0100 > > Add --print_statement checking capability to libtbx.find_clutter > > > ------------------------------ > > > d499b973be4c0443e607fbad13e495bb450938a3 > libtbx/command_line/find_clutter.py | 12 +++++++++++- > libtbx/file_clutter.py | 23 +++++++++++++++++++---- > 2 files changed, 30 insertions(+), 5 deletions(-) > > diff --git a/libtbx/command_line/find_clutter.py > b/libtbx/command_line/find_clutter.py > index 27baa6d7b..66f4b46eb 100644 > --- a/libtbx/command_line/find_clutter.py > +++ b/libtbx/command_line/find_clutter.py > @@ -13,6 +13,7 @@ def run(args): > only_dos = False > only_future = False > flag_absolute_import = False > + flag_print_statement = False > # > paths = [] > for arg in args: > @@ -34,6 +35,8 @@ def run(args): > only_future = True > elif (arg == "--absolute_import"): > flag_absolute_import = True > + elif (arg == "--print_statement"): > + flag_print_statement = True > else: > paths.append(arg) > if (len(paths) == 0): paths = ["."] > @@ -45,9 +48,12 @@ def run(args): > n_too_many_from_future_import_division = 0 > n_missing_from_future_import_absolute_import = 0 > n_too_many_from_future_import_absolute_import = 0 > + n_missing_from_future_import_print_statement = 0 > + n_too_many_from_future_import_print_statement = 0 > n_bad_indentation = 0 > for info in gather(paths=paths, find_unused_imports=not flag_ni, > - find_bad_indentation=flag_indentation, flag_absolute_import=flag_ > absolute_import): > + find_bad_indentation=flag_indentation, flag_absolute_import=flag_ > absolute_import, > + flag_print_statement=flag_print_statement): > if (info.is_cluttered(flag_x=flag_x)): > n_is_cluttered += 1 > if (info.n_bare_excepts > 0): > @@ -62,6 +68,10 @@ def run(args): > n_missing_from_future_import_absolute_import += 1 > elif info.n_from_future_import_absolute_import > 1: > n_too_many_from_future_import_absolute_import += 1 > + if info.n_from_future_import_print_statement == 0: > + n_missing_from_future_import_print_statement += 1 > + elif info.n_from_future_import_print_statement > 1: > + n_too_many_from_future_import_print_statement += 1 > if (info.bad_indentation is not None) and (flag_indentation) : > n_bad_indentation += 1 > info.show( > diff --git a/libtbx/file_clutter.py b/libtbx/file_clutter.py > index 8af972751..768f06491 100644 > --- a/libtbx/file_clutter.py > +++ b/libtbx/file_clutter.py > @@ -11,9 +11,12 @@ class file_clutter(object): > '^ from [ ]+ __future__ [ ]+ import [ \w,]+ division', re.VERBOSE) > from_future_import_absolute_import_pat = re.compile( > '^ from [ ]+ __future__ [ ]+ import [ \w,]+ absolute_import', > re.VERBOSE) > + from_future_import_print_statement_pat = re.compile( > + '^ from [ ]+ __future__ [ ]+ import [ \w,]+ print_statement', > re.VERBOSE) > > def __init__(self, path, find_unused_imports=False, > - find_bad_indentation=True, flag_absolute_import=False): > + find_bad_indentation=True, flag_absolute_import=False, > + flag_print_statement=False): > self.path = path > self.is_executable = os.access(path, os.X_OK) > self.dos_format = False > @@ -25,6 +28,8 @@ class file_clutter(object): > self.n_from_future_import_division = None > self.flag_absolute_import = flag_absolute_import > self.n_from_future_import_absolute_import = None > + self.flag_print_statement = flag_print_statement > + self.n_from_future_import_print_statement = None > self.bad_indentation = None > self.file_should_be_empty = False > bytes = open(path, "rb").read() > @@ -45,6 +50,7 @@ class file_clutter(object): > if (path.endswith(".py")): > self.n_from_future_import_division = 0 > self.n_from_future_import_absolute_import = 0 > + self.n_from_future_import_print_statement = 0 > py_lines = bytes.splitlines() > self.file_should_be_empty = True > for line in py_lines: > @@ -54,6 +60,8 @@ class file_clutter(object): > self.n_from_future_import_division += 1 > if self.from_future_import_absolute_import_pat.search(line): > self.n_from_future_import_absolute_import += 1 > + if self.from_future_import_print_statement_pat.search(line): > + self.n_from_future_import_print_statement += 1 > ls = line.strip() > if ( ls.startswith("except") > and ls[6:].strip().startswith(":") > @@ -103,7 +111,8 @@ class file_clutter(object): > if (self.has_unused_imports()): > sapp("unused imports=%d" % len(self.unused_imports)) > if self.file_should_be_empty: > - if self.n_from_future_import_division == 0 and > self.n_from_future_import_absolute_import == 0: > + if self.n_from_future_import_division == 0 and > self.n_from_future_import_absolute_import == 0 and \ > + self.n_from_future_import_print_statement: > sapp("file is empty, should be 0 byte file") > else: > sapp("file contains only 'from __future__ import' and should be > empty instead") > @@ -116,6 +125,11 @@ class file_clutter(object): > sapp("missing 'from __future__ import absolute_import'") > elif self.n_from_future_import_absolute_import > 1: > sapp("more than one appearance of 'from __future__ import > absolute_import'") > + if self.flag_print_statement and not self.file_should_be_empty: > + if self.n_from_future_import_print_statement == 0: > + sapp("missing 'from __future__ import print_statement'") > + elif self.n_from_future_import_print_statement > 1: > + sapp("more than one appearance of 'from __future__ import > print_statement'") > if (self.bad_indentation is not None) and (flag_indentation) : > n_tab, n_space = self.bad_indentation > sapp("non-standard indentation: %d space, %d tab" % (n_space, > n_tab)) > @@ -144,11 +158,12 @@ def is_text_file(file_name): > if (name.endswith(extension)): return True > return False > > -def gather(paths, find_unused_imports=False, find_bad_indentation=False, > flag_absolute_import=False): > +def gather(paths, find_unused_imports=False, find_bad_indentation=False, > flag_absolute_import=False, flag_print_statement=False): > clutter = [] > def capp(): > clutter.append(file_clutter(path, find_unused_imports, > - find_bad_indentation=find_bad_indentation, > flag_absolute_import=flag_absolute_import)) > + find_bad_indentation=find_bad_indentation, > flag_absolute_import=flag_absolute_import, > + flag_print_statement=flag_print_statement)) > for path in paths: > if (not os.path.exists(path)): > print >> sys.stderr, "No such file or directory:", path >

2 1

Scons for python3 released
by R. D. Oeffner 10 Oct '17

10 Oct '17

http://scons.org/scons-300-is-available.html Perhaps start using this to easy upgrading cctbx to python 3 -- 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

2 1

Re: [cctbxbb] [git/cctbx] master: Comment out simage test for moment as no one interested (apparently) in fixing test (767a45560)
by Nicholas Sauter 05 Oct '17

05 Oct '17

Graeme, Not true that we are not interested in fixing it. Billy just diagnosed the problem as of yesterday. I will provide a fix. 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 Wed, Oct 4, 2017 at 10:57 PM, 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 767a45560e5f5816d77e9f82e3f846a724967e81 > Author: graeme-winter <graeme.winter(a)gmail.com> > Date: Thu Oct 5 06:57:25 2017 +0100 > > Comment out simage test for moment as no one interested (apparently) > in fixing test > > > ------------------------------ > > > 767a45560e5f5816d77e9f82e3f846a724967e81 > rstbx/run_tests.py | 2 +- > 1 file changed, 1 insertion(+), 1 deletion(-) > > diff --git a/rstbx/run_tests.py b/rstbx/run_tests.py > index ea9de29e1..abaf74b4c 100644 > --- a/rstbx/run_tests.py > +++ b/rstbx/run_tests.py > @@ -19,7 +19,7 @@ def run(): > print "OK" > > tst_list = ( > - "$D/simage/tst.py", > + #"$D/simage/tst.py", > "$D/dps_core/tst_iotbx_converter.py", > "$D/diffraction/tst_predict.py", > "$D/diffraction/tst_ewald_sphere.py", >

1 0