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I think this has been reported before but when generating a map from a model using IMP::em::SampledDensityMap, the model and the map are not align.
I attached a code snippet below to recreate the issue.
In the test cases I have, the misalignment is up to 1.5Å, in each direction (~2.6Å total).
Added a test pdb here with figures to show the shift observed.
Left panel show the model and the generated map when opened in Chimera and the right panel shows the the aligned model and generated map after using Fit in Map tool from Chimera.
ATOM 2 CA ASN A 34 115.138 124.057 135.934 1.00 0.00 C
ATOM 10 CA SER A 35 113.093 124.043 139.143 1.00 0.00 C
ATOM 16 CA VAL A 36 116.390 122.713 140.875 1.00 0.00 C
ATOM 23 CA GLU A 37 117.654 126.453 140.524 1.00 0.00 C
ATOM 32 CA ARG A 38 114.654 127.291 142.635 1.00 0.00 C
ATOM 43 CA LYS A 39 115.520 124.680 145.361 1.00 0.00 C
I think this has been reported before but when generating a map from a model using IMP::em::SampledDensityMap, the model and the map are not align.
I attached a code snippet below to recreate the issue.
In the test cases I have, the misalignment is up to 1.5Å, in each direction (~2.6Å total).
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