[phenixbb] How to define multiple rebuilding region?
J J
phenix.upitt at gmail.com
Wed Jul 14 15:04:02 PDT 2010
Tom,
I have tried what you suggested.
*rebuild_chain_list= "A B"**rebuild_res_end_list= 50**rebuild_res_start_list=10*
or
*rebuild_chain_list= "A B"**rebuild_res_end_list= "50
50"**rebuild_res_start_list="10 10"*
*
*
Both do not work.
For 1st case, the error message says:
NOTE: No segments for chain 'A B' found.
Chains available: ['A', 'B']
The error message for the 2nd case says:
Sorry the string '10 10' cannot be interpreted as a residue number?
Am I missin something here?
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
> rebuild_res_start_list=10
>
> 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*>* ------------------------------------------------ *>* _______________________________________________*>* phenixbb mailing list*>* phenixbb at phenix-online.org <http://phenix-online.org/mailman/listinfo/phenixbb>*>* http://phenix-online.org/mailman/listinfo/phenixbb*
>
> Jason
> ------------------------------------------------
> University of Pittsburgh School of Medicine
> 3501 Fifth Avenue
> Pittsburgh, PA 15261
> ------------------------------------------------
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