Tapan Biswas

At what level of confidence with the model, using the model along map helps for auto sharpening?

Alejandro Buschiazzo

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)?

Ashok Nayak

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.

Ashok Nayak

thanks Tom. That answered my question!

Uwe Sauer

Maybe Tom said it in the beginning, but how do we generate the half-maps to start with?

Christopher Schlicksup

Hi Uwe, these would be part of the output from whichever software you used for cryo-EM single particle reconstruction

Wei Huang

Can we use the difference map between before and after DM to assign water molecule? Or structural water density still remains after DM?

Ashok Nayak

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?

Maulik Badmalia

How do we provide the symmetry file? For making symmetric models, upon checking the symmetry button it asks for the symmetry file.

Maulik Badmalia

That answers my question. Thank you!

Alejandro Buschiazzo

Is helical symmetry automatically handled in map2model? And, in those cases, can we benefit from map averaging (how to deal with that)?

Tapan Biswas

Could you please talk a bit about your experiences in tracing nucleic acids, particularly RNA?

Rajiv Singh

How to differentiate between a good fit and a over fit

Rajiv Singh

Any parameters and score that suggests fitting score

Alejandro Buschiazzo

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?

Maria Hrmova

Do you see alternate conformations of side chains in high-resolutions cryo-EM maps?

Alejandro Buschiazzo

Will it attempt building poly-ala at “mysterious” densities?

Maria Hrmova

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.

Rajiv Singh

Can we give stoichiometry of each molecules in Multiprotein complex for docking?

Alejandro Buschiazzo

Thanks a lot!! Was great

Rajiv Singh

Thank you so much for organising this workshop!

Brian Edwards

Thanks for a very educational workshop.

Uwe Sauer

Thanks for a very informative workshop!

Leah Braviner

Thank you for a very useful workshop!

Zoom Transcript