[phenixbb] Off Topic: Calculating accurately RMSD

Nigel Moriarty nwmoriarty at lbl.gov
Wed Oct 1 15:04:54 PDT 2014


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 at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Oct 1, 2014 at 2:36 PM, PC <patrick.cossins at 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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