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 : [email protected] Date : 02/10/2014 - 13:41 (GMTDT) To : [email protected] Cc : [email protected] Subject : Re: [phenixbb] Off Topic: Calculating accurately RMSD No I wanted the structure alignment RMSD but thank you. -----Original Message----- From: [email protected] Sent: Wed, 1 Oct 2014 15:47:09 -0700 To: [email protected] 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
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On Wed, Oct 1, 2014 at 3:21 PM, PC