[phenixbb] Autobuild with ligand in place?

Claudia Scotti claudiascotti at hotmail.com
Thu Apr 15 02:46:27 PDT 2010


Sorry for the probably easy question.

I'm trying to rebuild a model with Autobuild. The protein has a ligand, whose density is already well defined, thus that the input for the new autobuild run includes its coordinates as well. 

When I start the autobuild run, however, I see that the ligand is removed before rebuilding, which leads the program to use the ligand density to try to rebuild loops, thus introducing errors.

How can I keep the ligand in place, please? Or is there any alternative solutions?

Many thanks,


Claudia Scotti 
Dipartimento di Medicina Sperimentale 
Sezione di Patologia Generale 
Universita' di Pavia 
Via Ferrata, 1
27100 Pavia 
Tel. 0039 0382 986335/8/1 
Facs 0039 0382 303673

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