Hi Hari Only keyword you need (Assuming that you have aniso in your pdb)
refinement brefinement only Did you try the version (5.8 version) from our MRC-LMB wbesite. In older version refinement brefinement only would do isotropic refinement only. I think I have changed and to make sure that it works for mixed and aniso also. If 5.8 version does not do what you want please let me kno. regards Garib On 5 Sep 2013, at 17:06, hari jayaram wrote: > Hi Garib, > > Thanks for your help. I read the document at this location. > > Without "mixed" keyword the default iso "B"'s kick in, so this statement > below did not work. I took in a pdb with ANISO B's and ran a B-factor > refinement and outputs a PDB without ANISOU records for every atom > > # DId not work when I had anisou records for all atoms in input > refine- > bref bonly > > > This works and does the full anisotropic only refinement > refine- > bref aniso bonly > > > This also works ( I was just guessing before I saw your previoud email) but > It probably is equivalent to the one above. > refine- > bref anisoonly > > Thanks for your help > Hari > > > > > > > > On Thu, Sep 5, 2013 at 11:24 AM, Garib N Murshudov <ga...@mrc-lmb.cam.ac.uk> > wrote: > You do not need anisoonly. You need bref only. If input pdb has aniso card > then refmac will assume that mixed refinement should be done. If you want to > add aniso for some of the atoms then you can use instructions like: > > brefine mixed aniso residue 100 A atoms FE S C* > > > Please have a look documentation from the our LMB site for further details. > > Regards > Garib > > > On 5 Sep 2013, at 15:50, hari jayaram wrote: > >> Thanks Garib for the new version. >> >> For only an anisotropic B refinement ..what are the keywords. The one below >> seems to work >> refi - >> type REST - >> resi MLKF - >> meth CGMAT - >> bref anisoonly >> ncyc 5 >> >> As far as Bill Scotts question does coot not pick up refmac5 and libcheck >> from $CCP4_BIN ? >> >> Thanks >> Hari >> >> >> >> On Thu, Sep 5, 2013 at 10:15 AM, William G. Scott <wgsc...@ucsc.edu> wrote: >> On Sep 4, 2013, at 2:57 PM, Garib N Murshudov <ga...@mrc-lmb.cam.ac.uk> >> wrote: >> >> > You may need to use the latest available version (5.8) from our LMB site >> >> Hi Garib: >> >> Would it be possible to add a link for the source code, so this could also >> be used with Coot? >> >> Thanks. >> >> Bill >> > > Dr Garib N Murshudov > Group Leader, MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge > CB2 0QH UK > Email: ga...@mrc-lmb.cam.ac.uk > Web http://www.mrc-lmb.cam.ac.uk, > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > > > > > > > > > > > Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
