[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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