Dear Sonali, There is no such thing as an ideal rmsd for bonds and angles given resolution. IMO you should use rmsZ which also doesn't have an ideal value. If its below 1 your good. As for the isotropic vs anisotropic, you can use a hamilton test if you do two refinements changing only the B-factor model. Ethan Merritt had a paper about that last year in Acta D.
Now for the self plug: PDB_REDO automatically selects the B-factor model based on this test (and some more selectors) and will also optimize your weights to get proper rmsZ values for geometry. Cheers, Robbie Sent from my Windows Phone ________________________________ From: sonali dhindwal Sent: 2013-03-17 09:06 To: [email protected] Subject: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values Dear All, We want little suggestion and knowledge regarding refinement of data in Refmac. We have a data with resolution upto 1.5A. Overall redundancy of 5.5 and 3.7 in high resolution bin. and I over Sigma is also 21 overall and 2.2 in last resolution bin. When we first did isotropic refinement we used automatic weighing term, which gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and rmsAngle of 0.027 and 2.5 respectively. We were able to improve rmsBond and rmsAngle values by decreasing weighing term to 0.5. But when we do anisotropic refinement with weighing term of 0.5 it gives Rfree, Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle and rmsBond of 0.0074 and 1.25. Now, we want to know what should be the ideal values for rmsAngle and rmsBond at such resolution. Secondly, if we can use anisotropic refinement with such data. All your suggestions will be highly valuable. Thanks in advance. -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.”
