[phenixbb] Model required for combine_focused_maps

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Mon May 3 15:51:24 PDT 2021

Hi Fengwei,
The model has to be pretty good as it is used to evaluate the maps.   I
would improve the model first, at least by refinement , then combine the
maps, then maybe iterate the whole process with a new model.
-Tom T

On Mon, May 3, 2021 at 14:19 Zheng, Fengwei <Fengwei.Zheng at vai.org> wrote:

> Dear Phenix developers:
> Thank you for developing this so powerful and elegant software packages
> for our community!
> I am a newbie in cryoEM, and recently I got a consensus map, and split it
> into two parts to do the further focused refinement, after that I want to
> combine them together, and then to build my model, I learned that this
> "combine focused maps" module in Phenix can achieve this, I read through
> this online tutorial (
> https://www.phenix-online.org/documentation/reference/combine_focused_maps.html),
> for the starting input files, I seem need to provide my initial/consensus
> map, two focused maps and a model, but I have a question about this
> provided model:
> 1st,  need me to provide my final refined model (i.e. I need to finish my
> model building firstly according to my two focused maps), or I can use a
> homologue model for this combination?
> 2nd, if I use a homologue model that only can be roughly fitted into my
> consensus map, will this affect my final combination results?
> Appreciate!
> Best,
> Fengwei
> --
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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