usually something like fitmap #1 #0 search 100 radius 5 resolution 6 (old chimera syntax) after more or less moving the model where it ought to be. 

If I'm searching for something small like a ligand, I'll reduce "radius" to 0.5 or 1 (and obviously adjust/remove resolution) so it doesn't get sucked into protein density (maybe a "mask selection" keyword would also be helpful?).

Usually with these settings it'll be in the top several hits, depending on difficulty, symmetry etc

Cheers
Oli

On Dec 10, 2024, at 6:27 PM, Alexis Rohou <a.rohou@gmail.com> wrote:

+1 on that suggestion if it’s easily implemented, it would save some time

Also Oli, would you mind sharing what search settings you like to use? Do you often find the top result is a good fit, or do you end up browsing down the list?

On Tue, Dec 10, 2024 at 2:11 PM Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,

I frequently use fitmap with global search to quickly fit an initial model to low resolution EM maps at early stages of data processing. At low resolution, it is often not immediately obvious which hand of the map is correct, so I will fit to both the original map and one that has been Z-flipped. Would it be possible to add an option to do this automatically, similar to how the "resolution" flag fits a molmap of the model at the specified resolution to the map?

Cheers
Oli
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