Patrick

If you have a .geo (optionally from the end of phenix.refine) you can run a script I wrote to get the rmsd values for all, alt and not alt.

elbow.refine_geo_display model.geo

Time to parse 1.43


RMS results for model


RMS(D/Z)

             d-all          d-none         d-alt          z-all          z-none         z-alt          

  bond       0.001( 3550)   0.001( 3550)   0.000(    0)   0.051( 3550)   0.051( 3550)   0.000(    0)

  angle      0.532( 6399)   0.532( 6399)   0.000(    0)   0.182( 6399)   0.182( 6399)   0.000(    0)




Cheers

Nigel

---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Oct 1, 2014 at 2:36 PM, PC <patrick.cossins@inbox.com> wrote:
Hi,
Off topic-sorry
Is there a way to calculate RMSD 

1) Considering atoms in ALT conformations?
2) considering all atoms in the protein ?

PYMOL seems to be throwing atoms away.

Thank you
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