[phenixbb] How to define multiple rebuilding region?

Tom Terwilliger terwilliger at lanl.gov
Wed Jul 14 10:56:09 PDT 2010

Hi Jason,

Yes, the manual has some old text that goes with the now-unused GUI.  
Sorry about that.  I fixed it just last week.

I think you want to say something very similar to what you have below.  
The key is: the entries in these 3 lists must all correspond (i.e., 2  
numbers in each list). Try this:

rebuild_chain_list= " A   B "
rebuild_res_end_list= "50 50"
rebuild_res_start_list="10 10"

or else:

rebuild_res_end_list= 50

which should apply to all chains.

You should be able to use this approach to specify any number of  
regions to rebuild.

Let me know if that doesn't do it!
All the best,
Tom T

On Jul 14, 2010, at 11:42 AM, J J wrote:

> Dear All,
> I am trying to use phenix.autobuild to rebuild some poor regions in  
> my model.
> Since I know which part should be rebuilt, I was thinking using  
> rebuild_chain_list in combination with rebuild_res_end_list and  
> rebuild_res_start_list.
> The manual suggested: " You can specify more than one region by  
> using the Parameter Group Options button to add lines."  What is  
> this Parameter Group Options button? I am running through an .eff  
> file.
> I have tried something like this:
> rebuild_chain_list= " 'A, 'B' "
> rebuild_res_end_list= 50
> rebuild_res_start_list=10
> However, it does not work. It becomes more obscure to me what if I  
> want to rebuild more than one region in a single chain? Thanks in  
> advance.
> Jason
> ------------------------------------------------
> University of Pittsburgh School of Medicine
> 3501 Fifth Avenue
> Pittsburgh, PA 15261
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
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