EMDB initial contour level

[Tristan Croll]

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

[Tristan Croll]

API is described at https://www.ebi.ac.uk/pdbe/api/doc/emdb.html

On 2020-09-11 15:42, ChimeraX wrote:

[Tom Goddard]

I agree it would be nice to use the EMDB suggested contour level. A problem is that the user only fetches the map once, then it is cached in ~/Downloads/ChimeraX/EMDB. So ChimeraX would need to also cache the contour level (or better all the metadata), otherwise the next time the open that map it would not have the correct contour level. Potentially the meta data could be refetched but this slows down opening the data which would be a significant drawback.

Another issue that would need to be considered is how to handle when the EMDB REST service is not responding fast, or potentially it will be changed in the future and not respond at all. We have had several cases of discontinued web services that broke Chimera. ChimeraX ceasing to fetch EMDB maps or doing so very slowly waiting for a REST timeout would be very bad.

Another issue is that ChimeraX fetches EMDB maps from RCSB, PDBe or China depending on the user's location (host IP) and this REST meta-data service may only be from PDBe causing potential performance slowdown for users not in Europe.

Ideally the map data file would contain the meta-data to avoid all the above difficulties in making a robust implementation.

[Tom Goddard]

Done.

Fetching an EMDB map now always uses the recommended contour level in the EMDB meta-data if it is available. The map fetch now always fetches the XML meta-data file which is placed in ~/Downloads/ChimeraX/EMDB along side the map. I added the meta-data fetch to allow loading or logging fit PDB models (ticket #9846). It seemed that slowing down the fetch a little bit by getting this extra file was worth it since the fit PDBs and suggested contour level are valuable info.