At what level of confidence with the model, using the model along map helps for auto sharpening?
Tom, thanks, I have a question (for later) : How do phenix’s auto_sharpen results compare to the ones we can obtain within Coot (with coot’s sharpen/blurring tool)?
I have a question regarding variable rmsds in different cryoEM maps. How does one compare between two independent maps based on map rmsd? or its based on common sense to get the sigma best enough to see the sidechains well.
thanks Tom. That answered my question!
Maybe Tom said it in the beginning, but how do we generate the half-maps to start with?
Hi Uwe, these would be part of the output from whichever software you used for cryo-EM single particle reconstruction
Can we use the difference map between before and after DM to assign water molecule? Or structural water density still remains after DM?
In my case resolve DM improved the already high resolution parts of my map, but worsened the low resolution regions in my map. Is that normal?
How do we provide the symmetry file? For making symmetric models, upon checking the symmetry button it asks for the symmetry file.
That answers my question. Thank you!
Is helical symmetry automatically handled in map2model? And, in those cases, can we benefit from map averaging (how to deal with that)?
Could you please talk a bit about your experiences in tracing nucleic acids, particularly RNA?
How to differentiate between a good fit and a over fit
Any parameters and score that suggests fitting score
If I may: what if you have the sequence(s) of some components of a complex, but not of all: how should you go about using map2model?
Do you see alternate conformations of side chains in high-resolutions cryo-EM maps?
Will it attempt building poly-ala at “mysterious” densities?
Thanks for insights
Thank you Tom, this was well communicated and overall brilliant. Also thank you Paul for organising this workshop. Lots of parallel between x-ray and cryo-EM procedures.
Can we give stoichiometry of each molecules in Multiprotein complex for docking?
Thanks a lot!! Was great
Thank you so much for organising this workshop!
Thanks for a very educational workshop.
Thanks for a very informative workshop!
Thank you for a very useful workshop!