[phenixbb] phenix.reduce

Pavel Afonine pafonine at lbl.gov
Tue Aug 12 22:02:17 PDT 2008

Hi Mark,

I'm not 100% sure, but...

1) I think by default phenix.reduce adds H atoms to main conformations only;

2) You need to use "-ALLALT" option to ask it to add H to all 
conformations (type "phenix.reduce -h" for large list of options);

I hope the developers at Duke will provide their expert feedback on this...

Also (this I know for sure -:) ), if you use phenix.ready_set (Nigel is 
the author of it) then it will internally run phenix.reduce to add H to 
macromolecule and it will use its own jiffies to add H to ligands, plus 
it will create a cif file that will be consistent with all newly added 


On 8/12/2008 5:35 PM, Mayer, Mark (NIH/NICHD) [E] wrote:
> Hi,
> Does phenix.reduce correctly handle pdb files with alt confs?
> I ran reduce on such a file ang got a warning that only A was
> used, and when i checked output there were no H on AC B residues.
> I then  sent file to Molprobity server, ran reduce, and now there
> are H on residues for both ACs. 
> I'm doing this so I can refine with riding hydrogens.
> Thanks
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