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 : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov

On Wed, Oct 1, 2014 at 3:21 PM, PC <[email protected]> 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: [email protected]
Sent: Wed, 1 Oct 2014 15:04:54 -0700
To: [email protected]
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 : [email protected]
Fax   : 510-486-5909    Web : CCI.LBL.gov

On Wed, Oct 1, 2014 at 2:36 PM, PC <[email protected]> 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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