Re: [ccp4bb] anisotropic refinement
If we define high resolution as 1.2A and higher, there are ~1500 high-resolution entries (ignoring entries without experimental data). Of these ~1000 were refined with anisotropic B-factors by our method. We use the Hamilton R-ratio test to support our B-factor model choice. The ~1000 is an underestimate because the B-factor model used wasn't stored properly for the older entries. If more accurate numbers are needed, they can be mined from the PDB_REDO databank. HTH, Robbie Joosten Netherlands Cancer Institute www.cmbi.ru.nl/pdb_redo > Date: Thu, 11 Oct 2012 12:17:39 -0700 > From: merr...@u.washington.edu > Subject: Re: [ccp4bb] anisotropic refinement > To: CCP4BB@JISCMAIL.AC.UK > > On Thursday, October 11, 2012 11:50:37 am Rex Palmer wrote: > > Dear CCP4'ers > > With the occurrence of more and more high resolution protein structures > > does anyone know at present how many such structures have been successfully > > refined anisotropicall?� > > When we tried to categorize refinement protocols in the PDB at the end > of 2009 we identified about 1200 protein structures that had been given > full anisotropic treatment. Zucker et al, Acta Cryst. (2010). D66, 889–900 > > However, using automated search of the PDB it is hard to distinguish > full aniso refinement from structures refined with TLS but having missing > or malformed TLS records. > > As to "successfully", that's a separate question :-) > May Robbie Joosten has more recent numbers from the PDB-Redo project, > and a comment on success? > > Ethan > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > University of Washington, Seattle 98195-7742
Re: [ccp4bb] anisotropic refinement
On Thursday, October 11, 2012 11:50:37 am Rex Palmer wrote: > Dear CCP4'ers > With the occurrence of more and more high resolution protein structures does > anyone know at present how many such structures have been successfully > refined anisotropicall?� When we tried to categorize refinement protocols in the PDB at the end of 2009 we identified about 1200 protein structures that had been given full anisotropic treatment. Zucker et al, Acta Cryst. (2010). D66, 889–900 However, using automated search of the PDB it is hard to distinguish full aniso refinement from structures refined with TLS but having missing or malformed TLS records. As to "successfully", that's a separate question :-) May Robbie Joosten has more recent numbers from the PDB-Redo project, and a comment on success? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] anisotropic refinement
Dear CCP4'ers With the occurrence of more and more high resolution protein structures does anyone know at present how many such structures have been successfully refined anisotropicall? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] Anisotropic Refinement Question
Dear All, I appreciate the feed back from my question. I refined anisotropically without hydrogens and when I was satisfied with the model I added hydrogens with zero refinement cycles in REFMAC5. This worked equally well as adding hydrogens earlier in the refinement stage and keeping them present during the refinement. I have another question! I noticed that when adding hydrogens some have zero occupancies, examples are leucine CD hydrogens, isoleucine CD hydrogens and lycine NZ hydrogens. Is this a problem that I am generating without knowing it? Thank you, Carlos >>> "Arti S. Pandey" <[EMAIL PROTECTED]> 02/12/07 9:56 AM >>> Hey Carlos, Wouldnt refining anisotropically without hydrogens and then adding hydrogens work? The contribution to the lowering of R factor will still be there. > Dear Everyone, > > I have performed an anisotropic restrained refinement in REFMAC5 with > hydrogens added, and later read there is no need to refine the hydrogens > anisotropically. Is there a way to refine all atoms anisotropically > except hydrogens in REFMAC5? I would like to keep the hydrogens during > the refinement as they contribute to the R values. > > Sincerely, > Carlos > Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] Anisotropic Refinement Question
Dear Carlos When you add hydrogens in refmac they are used in geometry and structure factor calculations. They are not used in refinement fully. I.e. their contribution is taken into account and but they do not contribute to gradients and hessian. regards Garib On 12 Feb 2007, at 03:42, Carlos Huerta wrote: Dear Everyone, I have performed an anisotropic restrained refinement in REFMAC5 with hydrogens added, and later read there is no need to refine the hydrogens anisotropically. Is there a way to refine all atoms anisotropically except hydrogens in REFMAC5? I would like to keep the hydrogens during the refinement as they contribute to the R values. Sincerely, Carlos
Re: [ccp4bb] Anisotropic Refinement Question
Hey Carlos, Wouldnt refining anisotropically without hydrogens and then adding hydrogens work? The contribution to the lowering of R factor will still be there. > Dear Everyone, > > I have performed an anisotropic restrained refinement in REFMAC5 with > hydrogens added, and later read there is no need to refine the hydrogens > anisotropically. Is there a way to refine all atoms anisotropically > except hydrogens in REFMAC5? I would like to keep the hydrogens during > the refinement as they contribute to the R values. > > Sincerely, > Carlos > Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
[ccp4bb] Anisotropic Refinement Question
Dear Everyone, I have performed an anisotropic restrained refinement in REFMAC5 with hydrogens added, and later read there is no need to refine the hydrogens anisotropically. Is there a way to refine all atoms anisotropically except hydrogens in REFMAC5? I would like to keep the hydrogens during the refinement as they contribute to the R values. Sincerely, Carlos
