id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3708	EMDB initial contour level	Tristan Croll	Tom Goddard	"{{{
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

}}}
"	enhancement	closed	normal		Volume Data		fixed		Elaine Meng				all	ChimeraX