If you have a model from the PDB and you want to put it into your cryo-EM map, then you will need to first use either molecular replacement, real space automated fitting or real-space manual fitting (such as in Coot) to put your molecule in the right place. Then you can use phenix.real_space_refine to refine the model.

You can also use phenix.map_to_model, but that works in a different way. It tries to build your model from scratch (without reference to a known structure).

From: [email protected] <[email protected]> on behalf of Joshua Jude Lobo <[email protected]>
Sent: Thursday, August 10, 2017 8:50 AM
Cc: [email protected]
Subject: Re: [phenixbb] Appplying symmetry to a Cryo-EM map in phenix map_to _model

Hi Dr Terwilliger

I have the pdb of the asymmetric unit and I am trying to fit it into my cryo-EM map of the whole structure( which has octahedral symmetry). Do I have so to do some-sort of pdb manipulation before the model_to_map operation ?

This is my command

phenix.map_to_model postprocess_test.mrc 2w0o_1chain.pdb resolution=4 d_min_ratio=0.89 seq_file=2w0o.fasta.txt >> model_to_map.log

the fasta sequence and the pdb file are both of a single unit

I hope my question makes sense this is my first time using phenix ,

Sincerely

Joshua Lobo

On Sun, Aug 6, 2017 at 7:44 AM, Terwilliger, Thomas Charles <[email protected]> wrote:

Hi Joshua,

I'm sorry for the slow reply. In phenix.map_to_model you normally do not need to specify any space group information. (For cryo-EM we use "P1" as the "space group" but you don't have to specify it).

Let me know if that doesn't do it,

All the best,

Tom T

From: phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Joshua Jude Lobo <[email protected]>
Sent: Tuesday, August 1, 2017 12:50 PM
To: [email protected]
Subject: [phenixbb] Appplying symmetry to a Cryo-EM map in phenix map_to _model

Hi Phenix Group

I am very new to model building and using phenix . I am trying to use phenix.map_to_model to generate a model just using my cryo-EM map( mrc format) and a fasta sequence .My protein has octahedral symmetry . I found the use_space_group_symmetry argument but am not sure what argument to give to impose the symmetry .

Any inputs are appreciated

Sincerely

Joshua Lobo

University of Minnesota Twin Cities