Opened 5 years ago

Last modified 8 months ago

#3637 closed defect

ChimeraX bug report submission — at Initial Version

Reported by: Tristan Croll Owned by:
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Forwarded this to chimerax-bugs by email, but it's not showing up, so reporting via ChimeraX to ensure it doesn't get eaten by the system. The attached model was created from a larger model by:
- selecting all residues within a given radius from a point
- splitting into a temporary model using chimerax.std_commands.split.molecule_from_atoms
- moving all atoms by an offset
- writing to mmcif with provider_save()

The result fails to open in Phenix. Looks like the problem is that single-residue "helices" don't get annotated properly - their _struct_conf.beg_label_seq_id and _struct_conf.end_label_seq_id are each '.'.

Not a high priority for me - for this particular purpose the secondary structure is superfluous, so I can just clear it before writing.



OpenGL version: 3.3.0 NVIDIA 426.00
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: GL502VS
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 34,292,408,320
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: surrounding_model.cif

surrounding_model.cif​

Change History (1)

by Tristan Croll, 5 years ago

Attachment: surrounding_model.cif​ added

Added by email2trac

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