id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3337 Error assigning non-contiguous array to atom.bfactors Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0rc202005270557 (2020-05-27 05:57:28 UTC) Description A little bit of numpy weirdness going on: {{{ from chimerax.atomic import selected_atoms sel = selected_atoms(session) sel.bfactors.shape # (2,) sel.bfactors[::-1].shape # (2,) sel.bfactors = sel.bfactors[::-1] --------------------------------------------------------------------------- ValueError Traceback (most recent call last) in ----> 1 selected_atoms(session).bfactors = selected_atoms(session).bfactors[::-1] /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py in set_prop(self, values) 216 # Allocate numpy array of values to pass to C. 217 va = empty((n,value_count), value_type) --> 218 va[:] = values 219 v = pointer(va) 220 cset(self._c_pointers, n, v) ValueError: could not broadcast input array from shape (2) into shape (2,1) sel.bfactors = sel.bfactors # Fine import numpy sel.bfactors = numpy.require(sel.bfactors[::-1], requirements='C') # Fine }}} Log: UCSF ChimeraX version: 1.0rc202005270557 (2020-05-27) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open sCoat_AlF4_refine_13.pdb Chain information for sCoat_AlF4_refine_13.pdb #1 --- Chain | Description A | No description available > dssp > isolde start > set selectionWidth 4 Chain information for sCoat_AlF4_refine_13.pdb --- Chain | Description 1.2/A | No description available Done loading forcefield > set bgColor white Discarding unrecognised/unsupported data array /H8_4_1/H8_4_1/ISYM_H8_4_1 Y > addh Summary of feedback from adding hydrogens to sCoat_AlF4_refine_13.pdb #1.2 --- notes | No usable SEQRES records for sCoat_AlF4_refine_13.pdb (#1.2) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A ARG 41 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ARG 678 633 hydrogen bonds /A ARG 678 is not terminus, removing H atom from 'C' 4854 hydrogens added > hide HC > view :ALF > view :273 > select up 86 atoms, 83 bonds, 1 model selected > select up 268 atoms, 267 bonds, 1 model selected > select clear > select clear Updating bulk solvent parameters... > select #1 9577 atoms, 9625 bonds, 32 models selected > select clear Updating bulk solvent parameters... > color bfactor 9577 atoms, 662 residues, atom bfactor range 35.5 to 346 > ui tool show Shell /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") > color bfactor 9577 atoms, 662 residues, atom bfactor range 35.5 to 346 OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 8.6G 28G 243M 25G 53G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Core fixed Eric Pettersen all ChimeraX