[phenixbb] Off Topic: Calculating accurately RMSD

[Tim Gruene]

Hi all,

I was wondering if any of the suggested solutions calculate the
contribution to the RMSD of an atom with alternate coordinate as mean
weighted by occupancy? I would think this is what Mark is after. -Mark?

Best,
Tim

On 10/02/2014 04:28 PM, MARTYN SYMMONS wrote:
> rmsd command in chimera allows you to specify atoms in alternate conformations - 
> (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html) there is a bit of a learning curve in getting the selection syntax right.
> But I think it will only match the unique ones that you specify - not include all of a complete set of alternative confs,  which is maybe what you want.
> rmsd takes the existing superimposition - match will do a superimposition
>   all the best
>   Martyn 
> Cambridge  
> ----Original message----
> From : patrick.cossins at inbox.com
> Date : 02/10/2014 - 13:41 (GMTDT)
> To : nwmoriarty at lbl.gov
> Cc : phenixbb at phenix-online.org
> Subject : Re: [phenixbb] Off Topic: Calculating accurately RMSD
> No I wanted the structure alignment RMSD but thank you. 
> -----Original Message-----
> From: nwmoriarty at lbl.gov
> Sent: Wed, 1 Oct 2014 15:47:09 -0700
> To: patrick.cossins at inbox.com
> Subject: Re: [phenixbb] Off Topic: Calculating accurately RMSD
> 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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> 
> 
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-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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