+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 _______________________________________________ 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/

Hi Oli, I'm not sure what you envision this option doing. It will make an inverted copy of the map and run the same fit command on the inverted copy? And then you get a list of fits that includes ones in both maps? Sounds like a scripting task, basically expanding one command into 3. There is a tricky step of positioning the model in the inverted map. Not sure what you envision there, maybe the center (defined how?) of the model is placed at the corresponding point in the inverted map where it is in the original map. The task seems like a multi-step workflow and we generally don't put such things in as options to a command or in ChimeraX at all because there are such an immense number of examples of such workflows that would save the user from typing 3 commands instead of 1. It can't quite be done as an alias composed of the 3 commands since the model needs to be repositioned. I think the best route would be to make a Python script to do it. That script would compose the needed commands including positioning the model in the second map. Ideally I guess you'd want the list of fits sorted by score for both original orientation and flipped so the best from either search are at the top of the list but there is currently no ability to resort fit results, the second run fits are always appended to the first run. The sort could probably be done in a Python script. Maybe someone beside the core UCSF developers can take this on and contribute to ChimeraX as an extension. Tom

Hi Oliver, So if you want to flip the map and run fitmap search and it requires no repositioning of the model why not just an alias that runs those 2 commands? It is hard to make time for adding options that combine two commands into one unless hundreds of people will use it. And it complicates adding future features to the command. I'm working now on AlphaFold 3 support for ChimeraX which will have thousands of users. Still I do add small options if they help lots of users and allow something that can't be simply done already. I don't think this flipz before fitting is in that category. I would love to see other developers contribute that kind of feature if it is valuable to them. Tom

On Dec 10, 2024, at 6:23 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Tom,

For most EM maps, when doing a global search, there is no issue of recentering, as flipping the map doesn't change the center (and one typically just roughly positions the model in the center of the map)

Currently there is a keyword - resolution - which makes a molmap of the model and fits that and applies the same transformation to the model - I thought this was somewhat analogous (both being multi-step workflows). My thought with for example a "flipz" keyword would be that it would just flip the map and fit to it (rather than fitting to the original map), but as you say maybe not worth adding.

Cheers Oli

...

On Dec 10, 2024, at 8:38 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Oli,

I'm not sure what you envision this option doing. It will make an inverted copy of the map and run the same fit command on the inverted copy? And then you get a list of fits that includes ones in both maps? Sounds like a scripting task, basically expanding one command into 3. There is a tricky step of positioning the model in the inverted map. Not sure what you envision there, maybe the center (defined how?) of the model is placed at the corresponding point in the inverted map where it is in the original map.

The task seems like a multi-step workflow and we generally don't put such things in as options to a command or in ChimeraX at all because there are such an immense number of examples of such workflows that would save the user from typing 3 commands instead of 1. It can't quite be done as an alias composed of the 3 commands since the model needs to be repositioned. I think the best route would be to make a Python script to do it. That script would compose the needed commands including positioning the model in the second map. Ideally I guess you'd want the list of fits sorted by score for both original orientation and flipped so the best from either search are at the top of the list but there is currently no ability to resort fit results, the second run fits are always appended to the first run. The sort could probably be done in a Python script.

Maybe someone beside the core UCSF developers can take this on and contribute to ChimeraX as an extension.

Tom

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