[phenixbb] Appplying symmetry to a Cryo-EM map in phenix map_to _model

Terwilliger, Thomas Charles terwilliger at lanl.gov
Fri Aug 11 07:12:15 PDT 2017

?Hi Joshua,

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).

All the best,

Tom T

From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Joshua Jude Lobo <jlobo at umn.edu>
Sent: Thursday, August 10, 2017 8:50 AM
Cc: phenixbb at phenix-online.org
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 ,

Joshua Lobo

On Sun, Aug 6, 2017 at 7:44 AM, Terwilliger, Thomas Charles <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>> 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 at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> <phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>> on behalf of Joshua Jude Lobo <jlobo at umn.edu<mailto:jlobo at umn.edu>>
Sent: Tuesday, August 1, 2017 12:50 PM
To: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
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

Joshua Lobo
University of Minnesota Twin Cities

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