[phenixbb] Ramachandran results from Structure_comparison tool

Nigel Moriarty nwmoriarty at lbl.gov
Wed Mar 18 14:59:10 PDT 2015


It's because the Structure Comparison only shows you the residues that
differ between the models. It just so happens (and you can check this using
phenix.ramalyze) that all the residues after GLN 429 are in the same
favoured regions on the plot.



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

On Wed, Mar 18, 2015 at 10:49 AM, Emilia C. Arturo (Emily) <eca38 at drexel.edu
> wrote:

> Hello,
> I've just run the Structure comparison tool for the first time using
> phenix 1.9-1692. All the results tabs--except the Ramachandran
> tab--have per-residue values throughout the length of the ~450-residue
> sequence; the Ramachandran tab has values only through residue 429.
> The sequence file included with the run contains 453 residues. Each of
> the pdb files input to the run have between 445 and 450 residues each.
> Throughout the length of each model, all models are 100%
> sequence-identical to each other and to the sequence file.
> Is it a known bug, that the Ramachandran values are not output for all
> the residues for which there are values in the other tabs?
> Emily Arturo
> Ph.D. program in Biochemistry, Drexel Univ College of Medicine
> Jaffe lab, Fox Chase Cancer Center
> Philadelphia, PA
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