[phenixbb] How to define multiple rebuilding region?

J J phenix.upitt at gmail.com
Wed Jul 14 15:04:02 PDT 2010


I have tried what you suggested.

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


*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
> ------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100714/40343afa/attachment-0003.htm>

More information about the phenixbb mailing list