[phenixbb] Off Topic: Calculating accurately RMSD

[Nigel Moriarty]

Patrick

If you do a refinement in Phenix you get a .geo which contains the geometry
restraints information. It's a simple matter to calculate the rmsd of the
geometry restraints given that the model and ideal values are all listed.

Do you want a geometry restraints rmsd or a structure alignment rmsd?

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 3:21 PM, PC <patrick.cossins at inbox.com> wrote:

>  Hi Nigel,
>
> Could you tell me how you used the .geo file?
>
> In this I case I don't have a geo file but this might be useful in the
> future
>
>
> -----Original Message-----
> *From:* nwmoriarty at lbl.gov
> *Sent:* Wed, 1 Oct 2014 15:04:54 -0700
> *To:* patrick.cossins at inbox.com
> *Subject:* Re: [phenixbb] Off Topic: Calculating accurately RMSD
>
> 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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