Opened 5 years ago

Last modified 2 years ago

#3708 closed enhancement

ChimeraX bug report submission — at Initial Version

Reported by: Tristan Croll Owned by:
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Suggestion: use the depositor-recommended contour when opening a map from the EMDB. They have a convenient REST API for this: if you do, for example:

https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/EMD-2752

... it will return a JSON string including the recommended contour amongst other miscellaneous info:

{"EMD-2752":[{"map":{"origin":{"column":-112.0,"section":-112.0,"row":-112.0},"space_group_number":"1","statistics":{"standard_deviation":0.32400000000000001,"average":0.0201,"minimum":-8.4030000000000005,"maximum":9.766},"dimensions":{"column":224,"section":224,"row":224},"datatype":"Image stored as Reals","axis_order":{"slow":"Z","medium":"Y","fast":"X"},"spacing":{"column":224,"section":224,"row":224},"annotation_details":"reconstruction of ryanodine receptor 1 in partially open state","cell":{"a":{"units":"A","value":580.20000000000005},"c":{"units":"A","value":580.20000000000005},"b":{"units":"A","value":580.20000000000005},"beta":{"units":"degrees","value":90.0},"alpha":{"units":"degrees","value":90.0},"gamma":{"units":"degrees","value":90.0}},"limit":{"column":111.0,"section":111.0,"row":111.0},"details":"::::EMDATABANK.org::::EMD-2752::::","file":{"file_type":"map","value":"emd_2752.map.gz","size_kb":"43905","format":"CCP4"},"pixel_spacing":{"y":{"units":"A","value":2.5899999999999999},"x":{"units":"A","value":2.5899999999999999},"z":{"units":"A","value":2.5899999999999999}},"contour_level":{"source":"emdb","value":1.3100000000000001}}}]}

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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 19041)
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

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