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 ------------------------------------------------