[phenixbb] phenix.autobuild

[Paul Adams]

Hi Matt,

   I recommend updating to the latest version of PHENIX (1.3 final)  
from the web page.

   Cheers,	
	Paul

On Oct 23, 2008, at 3:10 AM, Matthew Chu wrote:

> Thank you for the detailed information Tom, my autobuild job is  
> actually running properly!
>
> Just some more minors questions:
> 1. AutoBuild Wizard will use phenix.elbow to generate geometries  
> for any ligands that are not recognized, but how can I find out  
> which ligands that can actually be recognized by phenix? Or to be  
> save, we better run elbow to generate the libraries for every  
> single ligands?
> 2. eLBOW can automatically add hydrogens to the input molecules if  
> there are less than a quarter of the possible hydrogens, however  
> this command doesn't work: phenix.elbow input_file.pdb --add- 
> hydrogens=True, and I can't find this option under the elbow manual?
> And actually I would like to remove those hydrogens so it should be  
> "add-hydrogens=false"? I am now using phenix-1.3-rc2.
> Thanks again!
>
> Matt
>
>
> -- 
> ---------------------------------------------------------------------- 
> ------
> Matthew LH Chu
> PhD Student
> School of Pharmacy and Pharmaceutical Sciences
> University of Manchester
> ---------------------------------------------------------------------- 
> ------
>
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-- 
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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