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 hydrogens. Pavel. 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

MLM

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