[phenixbb] Problems fitting NADH

Nigel Moriarty nwmoriarty at lbl.gov
Fri Mar 30 13:48:47 PDT 2012


Problems with non-tetrahedral phosphates can sometimes mean that the
starting geometry for the oxygens on the phosphates are switched. You
can check on possible problems in the .geo file. Look in the angle and
dihedral sections for large residuals.

I have attached a restraints file from the most recent version of
eLBOW in case that helps. I used

phenix.elbow --chemical-components=nai

If you still have trouble send me the files directly so I can investigate.


NB. Any files sent to me will be held in strictest confidence.

On Fri, Mar 30, 2012 at 1:21 PM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Fri, Mar 30, 2012 at 1:14 PM, Phillip Steindel <pstein at brandeis.edu> 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
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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