Hi Tim, It looks like you’ll need to navigate a bit of a learning curve using the available online resources (rather than me re-typing everything here!). Here are some useful pointers: 1) Phenix Video Tutorials: https://www.youtube.com/c/phenixtutorials There are several relevant tutorials on model building. 2) Self-Guided Tutorials: Phenix comes with built-in tutorials, including many focused on model building. You’ll see examples of how to use them in the video tutorials mentioned above. 3) Phenix Documentation: https://phenix-online.org/documentation/ It provides plenty of detailed guidance and references. 4) Workshops for Hands-On Experience. Consider attending one of upcoming workshops with Phenix experts: - ACA Satellite Phenix Workshop (Summer 2025); - Week-long Crystallography & Cryo-EM School in Madrid (Spring 2025); - Mini Phenix Workshop at the West Coast Structural Biology Meeting (Spring 2025); ...and I’m sure more will be coming in 2025. Please reach out if you have specific questions that aren’t covered in these resources. Good luck! Pavel On 12/18/24 09:49, tim smith wrote:

Hi all,

Can you please advise once we fit the map and open in coot. What is next step to do in coot. I tried refmac but that required ccp4 file which doesn't have. Please some one can help in elaborating and sharing any tutorial would be helpful. I'm new bie and first time I am trying model building. Any help would be really appreciated. Thank you so much Best wishes Tim

On Tue, 17 Dec 2024, 13:47 Oleg Sobolev, wrote:

Hello Iram,

The general workflow for Cryo-EM is described here: https://phenix-online.org/documentation/overviews/cryo-em_index.html

It looks like you are ready to refine your model, so the tool for it is phenix.real_space_refine: https://phenix-online.org/documentation/reference/real_space_refine.html that also has a video tutorial.

Let us know if you have any questions.

Best regards, Oleg Sobolev.

On Thu, Dec 12, 2024 at 5:54 PM iram aziz wrote:

Hello All.       I got a nice 2.45 Angstrom map from cryo em data. I checked handedness, map model fitting on the chimera and opened in the coot. It looks nice. Can you please give me suggestions about the Phenix refinement steps. Thanks Iram _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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hello On Wed, Dec 18, 2024, 8:26 PM Dorothee Liebschner wrote:

Hi Iram,

A good place to start is to read the documentation for tools in cryo-EM: https://phenix-online.org/documentation/overviews/cryo-em_index.html

We also have a couple of video tutorials on our youtube channel ( https://www.youtube.com/@PhenixTutorials), for example for phenix.real_space_refine: https://www.youtube.com/watch?v=shmBHtyUdCc

Best wishes,

Dorothee

On Thu, Dec 12, 2024 at 5:54 PM iram aziz wrote:

...

Hello All. I got a nice 2.45 Angstrom map from cryo em data. I checked handedness, map model fitting on the chimera and opened in the coot. It looks nice. Can you please give me suggestions about the Phenix refinement steps. Thanks Iram _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

-- Dorothee Liebschner, PhD (she/her) Research Scientist Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Road https://www.google.com/maps/search/1+Cyclotron+Road?entry=gmail&source=g , M/S 91R0183 Berkeley, CA 94720 Web: https://phenix-online.org _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s