- cctbxbb - phenix-online.org

What does get numpy to be install during bootstrap?
by Luc Bourhis 14 Dec '17

14 Dec '17

Hi, I noticed that bootstrap.py does indirectly result in the installation of numpy but a quick swipe of the code did not reveal to me what does get it installed. Since I am sure somebody knows… Best wishes, Luc

2 1

Fwd: [Dials-support] dials.stills_process crash report
by Graeme.Winter＠diamond.ac.uk 13 Dec '17

13 Dec '17

Folks Once again, lack of stack traces in easy_mp is a big annoyance I forget the reasons why printing the actual error was a bad thing, but I do remember a discussion some 18 mo past Not wishing to replay the entire transaction, but could we revisit this? Thanks Graeme Begin forwarded message: From: <Danny.Axford(a)Diamond.ac.uk<mailto:[email protected]>> Subject: [Dials-support] dials.stills_process crash report Date: 12 December 2017 at 17:43:41 GMT To: <dials-support(a)lists.sourceforge.net<mailto:[email protected]>> Cc: martin.appleby(a)diamond.ac.uk<mailto:[email protected]> Perhaps this means something to someone. This is the SACLA data again, it seems to run happily and then hit a problematic frame? Martin and I see the error at pretty much the same point in the dataset, we were both running on local machines rather than the cluster. Cheers, Danny Detector 1 RMSDs by panel: ---------------------------------------------------- | Panel | Nref | RMSD_X | RMSD_Y | RMSD_DeltaPsi | | id | | (px) | (px) | (deg) | ---------------------------------------------------- | 1 | 89 | 0.37442 | 0.48949 | 0.2192 | | 2 | 69 | 0.49627 | 0.4847 | 0.21385 | | 5 | 90 | 0.48267 | 0.59909 | 0.22839 | | 6 | 70 | 0.6094 | 0.55592 | 0.20944 | ---------------------------------------------------- Traceback (most recent call last): File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/build/../modules/dials/command_line/stills_process.py", line 870, in <module> halraiser(e) File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/build/../modules/dials/command_line/stills_process.py", line 868, in <module> script.run() File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/build/../modules/dials/command_line/stills_process.py", line 383, in run preserve_exception_message=True) File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/modules/cctbx_project/libtbx/easy_mp.py", line 623, in parallel_map result = res() File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/modules/cctbx_project/libtbx/scheduling/result.py", line 119, in __call__ self.traceback( exception = self.exception() ) File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/modules/cctbx_project/libtbx/scheduling/stacktrace.py", line 86, in __call__ raise exception RuntimeError: Please report this error to dials-support(a)lists.sourceforge.net<mailto:[email protected]>: exit code = -9 -- 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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://slashdot.org/>! http://sdm.link/slashdot _______________________________________________ DIALS-support mailing list DIALS-support(a)lists.sourceforge.net<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/dials-support

3 2

Re: [cctbxbb] cctbxbb Digest, Vol 105, Issue 3
by Mooers, Blaine H.M. (HSC) 08 Dec '17

08 Dec '17

Hi Gianluca , You might try getting the sources for 2.7 from here: https://gist.github.com/0x414A/8b64178e69d9f8331938 Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage X-ray lab (LBSF) COBRE in Structural Biology SSRL UEC Facebook Page SSRL UEC SSRL SAC LCLS UEC EasyPyMOL Molecular Graphics Small Angle Scattering office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of cctbxbb-request(a)phenix-online.org [cctbxbb-request(a)phenix-online.org] Sent: Friday, December 08, 2017 2:00 PM To: cctbxbb(a)phenix-online.org Subject: cctbxbb Digest, Vol 105, Issue 3 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. Importing PyQt4 in litbx.python (Gianluca SANTONI) 2. Re: Importing PyQt4 in litbx.python (markus.gerstel(a)diamond.ac.uk) 3. Re: Importing PyQt4 in litbx.python (Gianluca SANTONI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 8 Dec 2017 13:18:13 +0100 From: Gianluca SANTONI <gianluca.santoni(a)esrf.fr> To: cctbx mailing list <cctbxbb(a)phenix-online.org> Subject: [cctbxbb] Importing PyQt4 in litbx.python Message-ID: <09889a85-3126-af38-05f3-8af190cdfd07(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) ------------------------------ Message: 2 Date: Fri, 8 Dec 2017 12:40:13 +0000 From: <markus.gerstel(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] Importing PyQt4 in litbx.python Message-ID: <f8d53c3e-c8d8-4941-9540-c9b80f95441d(a)email.android.com> Content-Type: text/plain; charset=utf-8 Hi, There is an issue open on UCS4 which is somewhat related: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… We currently don't use UCS4, and your system pyqt4 does. You would have to install (and potentially, compile) it for the cctbx python directly. A 3 minute research from my mobile phone suggests that you might be able to download the sources as tar.gz files and then do something along the lines of cctbx.python -m pip install SIP cctbx.python -m pip install pyqt-source.tar.gz but this is untested, and I haven't used pyqt before. -Markus On 8 Dec 2017 12:19, Gianluca SANTONI <gianluca.santoni(a)esrf.fr> wrote: Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… -- 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 ------------------------------ Message: 3 Date: Fri, 8 Dec 2017 14:20:26 +0100 From: Gianluca SANTONI <gianluca.santoni(a)esrf.fr> To: cctbxbb(a)phenix-online.org Subject: Re: [cctbxbb] Importing PyQt4 in litbx.python Message-ID: <820c8b08-d380-dd46-e25a-e9ee9e4b076b(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Hi Markus, I could fix everyting by compiling both libraries from source with cctbx.python. Hope this helps others with similar problem too. cctbx.python -m pip install SIP cctbx.python -m pip install pyqt-source.tar.gz did not work. There is actually no PyPi package for sip in python2.7 Cheers Gian Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) On 08/12/2017 13:40, markus.gerstel(a)diamond.ac.uk wrote: > Hi, > > There is an issue open on UCS4 which is somewhat related: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… > > We currently don't use UCS4, and your system pyqt4 does. You would have to install (and potentially, compile) it for the cctbx python directly. > > A 3 minute research from my mobile phone suggests that you might be able to download the sources as tar.gz files and then do something along the lines of > > cctbx.python -m pip install SIP > cctbx.python -m pip install pyqt-source.tar.gz > > but this is untested, and I haven't used pyqt before. > > -Markus > > On 8 Dec 2017 12:19, Gianluca SANTONI <gianluca.santoni(a)esrf.fr> wrote: > Dear all, > I'm having some troubles recently in importing pyqt4 in libtbx.python > under Debian8. > It used to work with a previous build compiled from the sources, but I > don't find a reasonable way to make it work from the bootstrap installation. > > More details: > > 1) If I do in libtbx.python > sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 > import QtCore", I get an > > unidentified symbol: PyUnicodeUCS4_AsLatin1String > > 2) If I try to compile cctbx as I did in the past "python > ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm > missing something > > Thanks everybody for your help. > Gian > > -- > Gianluca Santoni, PhD > ESRF structural biology group > 71 avenue des Martyrs > 38027 Grenoble cedex (France) > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > ------------------------------ _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… End of cctbxbb Digest, Vol 105, Issue 3 ***************************************

1 0

Re: [cctbxbb] Importing PyQt4 in litbx.python
by markus.gerstel＠diamond.ac.uk 08 Dec '17

08 Dec '17

Hi, There is an issue open on UCS4 which is somewhat related: https://github.com/cctbx/cctbx_project/issues/60 We currently don't use UCS4, and your system pyqt4 does. You would have to install (and potentially, compile) it for the cctbx python directly. A 3 minute research from my mobile phone suggests that you might be able to download the sources as tar.gz files and then do something along the lines of cctbx.python -m pip install SIP cctbx.python -m pip install pyqt-source.tar.gz but this is untested, and I haven't used pyqt before. -Markus On 8 Dec 2017 12:19, Gianluca SANTONI <gianluca.santoni(a)esrf.fr> wrote: Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org 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

2 1

Importing PyQt4 in litbx.python
by Gianluca SANTONI 08 Dec '17

08 Dec '17

Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France)

1 0

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