cctbx_project
cctbx_project copied to clipboard
cctbx
Computational Crystallography Toolbox
Hello, I got these syntax warning during the installation of cctbx with dials ``` Paramétrage de python3-dials (2.2.1+dfsg2-1) ... /usr/lib/python3/dist-packages/mmtbx/hydrogens/__init__.py:237: SyntaxWarning: "is not" with a literal. Did you mean "!="?...
Hi, I'm trying to align a pair of pdb/mtz files using the phenix.superpose_maps function and I was wondering if there was a way to fix the positions of one structure,...
... and if this is deprecated and changed by the user a deprecation warning emitted - see https://github.com/dials/dials/pull/1207#issuecomment-604289311 for inspiration
It looks like the unit cell standard deviations are calculated using the input unit cell parameters, rather than after being mapped to the niggli cell, as demonstrated by the following...
``` from __future__ import print_function from cctbx import sgtbx from cctbx.sgtbx.lattice_symmetry import metric_subgroups cs = sgtbx.space_group_info("I23").any_compatible_crystal_symmetry(volume=100000) print("cs:", cs, "\n") subgroups = metric_subgroups(cs, max_delta=5, bravais_types_only=False) print("input_symmetry:", subgroups.input_symmetry) for i in range(len(subgroups.result_groups)):...
Test in #421 is failing, but libtbx testing mistakenly treats it as success and only notes the standard error output. The test is not listed in the "This-is-broken-this-is-fine" category. ```...
There is an inconsistency regarding the default arguments of `clashscore.py`, in particular `condensed_probe`. Running the python script on a molecule produces slightly different results than running the validation in PHENIX....
The command line args for `programs/clashscore.py` differ between overview and details. In particular `b_factor_cutoff=40` and `b_factor_cutoff = None\n .type = int`. https://github.com/cctbx/cctbx_project/blob/34685978dccbf7a194fe99be48a51c2c99244c07/mmtbx/programs/clashscore.py#L24-L26 vs. https://github.com/cctbx/cctbx_project/blob/34685978dccbf7a194fe99be48a51c2c99244c07/mmtbx/programs/clashscore.py#L66-L69
I am not sure how prevalent the ```raise_if_errors``` is in the code base, but it recently got me on a harmless versioning error akin to [this](https://stackoverflow.com/a/156387/2077270). I was trying to...
I'm bootstrapping on a fresh Ubuntu 17.10 VM, `gcc 7.2.0`. The base installation fails on `glib` with: ``` CC libglib_2_0_la-gdate.lo gdate.c: In function 'g_date_strftime': gdate.c:2497:7: error: format not a string...
