On Fri, Mar 30, 2012 at 1:14 PM, Phillip Steindel wrote:

Dear all,

I'm trying to fit a NADH into a 1.7 Å structure.  LigandFit worked with just the three-letter code (NAI), however phenix.refine won't work with just the model. If I use eLBOW to create restraints, meanwhile, the ligand gets distorted during refinement (non-tetrahedral phosphates, mainly).  I'm not sure exactly how I'm supposed to be generating these restraints- any help is appreciated.  Thank you,

What did you use as input for eLBOW? Assuming the ligand geometry output by LigandFit is okay, you might want to include this as input to eLBOW as the final geometry, along with NAI as the chemical components code. -Nat

Hi Phillip, You have to check your ligand geometries in reel, and do modifications accordingly of your pdb file. Sometimes the submitted pdb files in the database does not have right bonds. Alternatively try generating your restraints using smilestrings instead of pdb it always works better. HTH, Shya On Fri, Mar 30, 2012 at 4:14 PM, Phillip Steindel wrote:

Dear all,

I'm trying to fit a NADH into a 1.7 Å structure. LigandFit worked with just the three-letter code (NAI), however phenix.refine won't work with just the model. If I use eLBOW to create restraints, meanwhile, the ligand gets distorted during refinement (non-tetrahedral phosphates, mainly). I'm not sure exactly how I'm supposed to be generating these restraints- any help is appreciated. Thank you,

Phillip Steindel Theobald Lab Department of Biochemistry Brandeis University _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb