Hi,
I have a few datasets that will have unique depositions, and was hoping to deposit them in the correct alignment/register. I can perfectly align the maps in ChimeraX, but ‘Align 3D Maps’ in CryoSPARC doesn’t quite work.
In grey (dataset1) is the reference map, cyan (dataset2) is a A3DM map that is just slightly offset, yellow (dataset3) is a correctly oriented A3DM map but translated quite far from the grey map. I’ve tried to connect the output of one round of A3DM to a subsequent round, but the output is exactly the same as the first, so it seems to me like the A3DM results are very close but get “stuck” in some minima.
I have some variable pixel sizes for these datasets, so resampling in ChimeraX leads to artifacts when I go to redo the 3D refinement.
Would appreciate some guidance/tips!
Thanks,
David
Are you using a mask for the alignment? And have you tried playing with the resolution for alignment? Definitely Align3D can be a bit finicky sometimes…
if you have PDBs for the 2 maps, you could align the PDBs and use the matrix to transform the maps, I think Phenix has a tool for that.
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Yes - matrixcopy - have used that before. You use it after matchmaker to apply the same transformation to the map as to the model
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Thank you for your replies.
I have tried A3DM with/without masks, and various low-pass filters (3 - 12 A), and the result is the exact same each time (at least for the cyan → grey alignment example).
Are you referring to the Phenix ‘Superpose maps’ job? I found this thread (superpose CryoEM map onto an Xray map? - phenixbb - phenix-online.org) that describes first converting your MRC maps to MTZ maps for the job, though Pavel mentions that there are still artifacts that can propagate if the maps are not on the same grid. I don’t see where it accepts a matrix file, and I tried matrixcopy with ChimeraX, but that command does not seem available anymore – is there an updated one you can share? I found matchmaker in ChimeraX has the ‘Log tranformation matrix’ checkbox in the Fitting tab, is that sufficient?
I appreciate your help!
Hi,
I am not sure if there is an implementation of matrixcopy in ChimeraX - it is present in Chimera, which still works fine 
I wasn’t referring to superpose maps in Phenix, just to resampling maps in Chimera. This would be at the end of your workflow - after refinement. I wouldn’t redo refinement after aligning, as this may subtly mess up the alignment (assuming you are starting refinement at a relatively low resolution).
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Hi again,
I have been reading through Kleywegt et al., 2024 (DOI: 10.1107/S2052252524001246), and was hoping to satisfy the recommendations list. So, by resampling maps in Chimera onto a reference map, how can I also deposit the relevant masks/half-maps/particle stacks?
Thanks again,
David
You can apply the same transformation (using matrixcopy) to the half-maps/masks, and resample on the same grid. Or just live with them unaligned.
Those recommendations are good general guidelines; but there are always going to be exceptions, which is fine if they are well reasoned & rationalized, just explain what you have done and why (IMHO).
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