Hi Tom, the way I would envision it working is that when you perform a fitmap search with a certain flag (--test_zflip or similar), it creates a z-flipped copy of the map to fit and runs two fitmap searches (one on the original and one on the flipped copy), presenting the results in a unified fit list, with the matches to the z-flipped map flagged as such in the fit list. I'm not sure whether that is practical to implement or not, but the functionality would be useful I think Cheers Oli
On May 19, 2026, at 8:42 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
Seems like a reasonable idea although I'm not clear on how the details would work. You have many maps, and would there be explicit flipped copies, and what would the GUI for the search results show that is different from what it shows now if you do multiple fitmap search commands?
Tom
On May 18, 2026, at 12:22 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to suggest a possible enhancement for fitmap that would be useful in cryoEM workflows - optionally searching both the original map, and a z-flipped copy.
In cryoEM, we often obtain initial reconstructions using ab initio reconstruction, which may converge on either the correct or inverted hands, and at low resolution, it is sometimes difficult to distinguish which (if any) is a correct solution - often, unambiguous fit of an atomic model is helpful to confirm that one has a correct solution. Fitmap with global search (e.g. fitmap #1 in #2 search 100 radius 5) is useful to get an initial fit list.
It would therefore be convenient if fitmap had an option to automatically test the fit of a model vs both the selected map and a z-flipped copy.
We do this now by pre-flipping the map and doing two searches (one against each copy), but when all the classes are loaded from a classification job this can become a bit unwieldy, in terms of keeping track of which map ID corresponds to the flipped copy of which map.
Cheers Oli _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/