[ccp4bb] B-iso vs. B-aniso
Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable gap for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts and/or opinions from the community are welcome. Cheers,
Re: [ccp4bb] B-iso vs. B-aniso
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear, 1.24A resolution is reasonable for anisotropic refinement - including restraints you have more observations than the number of reflections, so just doing the calculation does not give a concise answer! You should try and see if the refinement is stable and makes sense (e.g. check the number of npd-atoms etc.) You may also try the RIGU command in the beta-version of shelxl (Acta Cryst. (2012). A68, 448-451)! Regards, Tim On 09/17/2012 08:31 PM, Yuri Pompeu wrote: Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable gap for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts and/or opinions from the community are welcome. Cheers, - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQV284UxlJ7aRr7hoRAh5FAJ43TevZbbQLYGeE1yM2cqKjZ5KMFACg5bCs Ijn4owVvuuHldNSnK4Iax1E= =4Jdg -END PGP SIGNATURE-
Re: [ccp4bb] B-iso vs. B-aniso
On Monday, September 17, 2012 11:31:53 am Yuri Pompeu wrote: Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable gap for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? I laid out my thoughts on this topic at last year's CCP4 Study Weekend. The print version of it may be found here: To B or not to B: a question of resolution? Acta Cryst. D68, 468-477. http://dx.doi.org/10.1107/S0907444911028320 One lesson is that lower R-work and R-free does not necessarily indicate that anisotropic refinement is justified. In other words, it is not so easy to determine how much improvement is significant improvement. Any thoughts and/or opinions from the community are welcome. Cheers, -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] B-iso vs. B-aniso
Dear Yuri, Why do you think you need 36 reflections per atom when atoms with anisotropic B-factors only have 9 parameters? You can get away with much fewer in many cases especially if you have good restraints. As Ethan points out, a drop in R-free after adding many parameters may be misleading. Proper testing will give you a clearer example. The Hamilton test in Ethan's paper is implemented in PDB_REDO (http://scripts.iucr.org/cgi-bin/paper?ba5174) and I had a quick look at some refinement statistics for structures with ~21 reflections/atom (like your case): according to PDB_REDO's strict criteria anisotropic B-factors are acceptable in two thirds of the cases. This was tested with Refmac on 285 PDB entries; ShelX's new restraints may well increase the success rate. HTH, Robbie Joosten Netherlands Cancer Institute www.cmbi.ru.nl/pdb_redo -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri Pompeu Sent: Monday, September 17, 2012 20:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] B-iso vs. B-aniso Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space- group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable gap for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts and/or opinions from the community are welcome. Cheers,
