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option to turn off the mass match in alignto() #2285

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xiki-tempula opened this issue Jul 5, 2019 · 3 comments

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@xiki-tempula
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commented Jul 5, 2019

Is your feature request related to a problem? Please describe.
When one might want to convert the coarse-grain simulation to atomistic simulation, one will usually align the crystallographic protein to the coarse-grain protein.

Describe the solution you'd like
Ideally, this should be done using

from MDAnalysis.analysis.align import alignto
alignto(AT.atoms, CG.atoms, select=('name CA', 'name BB'))

However, since the mass of the CG backbone bead has a different mass from the CA atoms, the error MDAnalysis.exceptions.SelectionError: Inconsistent selections, masses differ by more than 0.1; mis-matching atoms are shown above.
is raised and there isn't a way of turning this off.

@orbeckst

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commented Jul 12, 2019

A dirty workaround should be to set tol_mass=1000 in alignto().

@orbeckst

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commented Jul 16, 2019

@xiki-tempula did this do anything for you?

@xiki-tempula

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commented Jul 16, 2019

@orbeckst Thank you for the information. I kind of just did my own fork and move the raise exception part to the actions under strict keyword, so if strict=False then the exception won't get raised. However, I do notice that strict=False is set to False by Default so my method of disabling the mass checking when strict=False might not be good for naive users. Thus, I raise an issue and hope to see what are people's opinion on this.

@orbeckst orbeckst changed the title Is it possible to turn off the mass match in alignto()? option to turn off the mass match in alignto() Jul 18, 2019

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