Closed dennisbrookner closed 1 year ago
I think this is because Coot thinks your map is "EM" map. If alpha=beta=gamma=90 and P1, Coot considers it an EM map and doesn't show symmetry. https://github.com/pemsley/coot/blob/523de831e062e10af6c4c06b442da5ab7c40e507/src/molecule-class-info-maps.cc#L2155
That makes sense, thanks!
Do you know if there's a way to override that when you open the map in Coot?
I don't think we can. It is great that you opened an issue on coot. Actually I also wanted that feature.
Closing this issue now that I've got a response from coot. Thanks!
https://github.com/pemsley/coot/issues/67#issuecomment-1336489684
Hey gemmi team,
I've encountered something puzzling in my work with real-space maps (
gemmi.FloatGrid
andgemmi.Ccp4Map
objects) which seem to sometimes lose periodic boundary conditions. To reproduce this behavior, I am starting with two mtz files from the PDB,1rx2_phases.mtz
and7mm1_phases.mtz
. Importantly for these purposes,1rx2
is inP 21 21 21
and7mm1
is inP 32 2 1
. These files are in the zip archive below, or can be downloaded from the PDB.input mtzs
The behavior I observe is as follows:
1rx2
to a P 21 21 21 map: everything works as expected. Map has periodic boundary conditions.1rx2
to a P 1 map: when I open this map in coot, electron density only appears inside the unit cell, and abruptly disappears outside the unit cell. E.g., this map no longer has periodic boundary conditions.7mm1
to a P 32 2 1 map: I get an error when I attempt to open this map in coot. Upon inspecting this map in python, I'm unable to find anything wrong with it, but something isn't working.7mm1
to a P 1 map: everything works as expected. Map has periodic boundary conditions.Below is the code I used to create these four map files from the input mtzs. The code uses a mixture of
reciprocalspaceship
andgemmi
functionality. I have linked to thereciprocalspaceship
source code where relevant. I have observed this behavior with bothgemmi 0.5.5
andgemmi 0.5.7
. Hopefully, this code is runnable without issue with a simplepip install reciprocalspaceship
and thenpython thisfile.py *.mtz
.I'm not sure whether this behavior is 1) a bug, 2) an error in my usage, or 3) the intended behavior for a reason that I'm not understanding. I appreciate the time, and I would love to know how to write a map in either P1 or the original spacegroup and maintain the desired periodic boundary conditions. Thanks so much! Let me know if there's any more information I should include!
Here is the code I used: