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

Joshua Jude Lobo jlobo at umn.edu
Thu Aug 10 07:50:12 PDT 2017

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> 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 <phenixbb-bounces at phenix-
> online.org> on behalf of Joshua Jude Lobo <jlobo at umn.edu>
> *Sent:* Tuesday, August 1, 2017 12:50 PM
> *To:* 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
> Sincerely
> Joshua Lobo
> University of Minnesota Twin Cities
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