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@inbox.com
Date : 02/10/2014 - 13:41 (GMTDT)
To : nwmoriarty@lbl.gov
Cc : phenixbb@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@lbl.gov
Sent: Wed, 1 Oct 2014 15:47:09 -0700
To: patrick.cossins@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@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Oct 1, 2014 at 3:21 PM, PC <patrick.cossins@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@lbl.gov
Sent: Wed, 1 Oct 2014 15:04:54 -0700
To: patrick.cossins@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@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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