Re: [ccp4bb] Only refine Bs in Refmac?
What has happened to the CCP4 update procedure? Shouldnt this mean latest versions are on that web site? e On 4 September 2013 22:57, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote: Hi refine bref bonly should be what you are looking for. You may need to use the latest available version (5.8) from our LMB site: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ With best regards Garib On 4 Sep 2013, at 19:59, hari jayaram wrote: Hi, How does one only refine Bs in refmac without changing the model coordinates . Is this accomplished using a zero cycle refinement with b-refinement set. I have never had to do this till now and didnt know how to set it up. Thanks Hari 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/
Re: [ccp4bb] Only refine Bs in Refmac?
It should be on the latest ccp4. But as I understand ccp4 people extremely busy to make the latest version of ccp4 available. Regards Garib On 5 Sep 2013, at 10:36, Eleanor Dodson wrote: What has happened to the CCP4 update procedure? Shouldnt this mean latest versions are on that web site? e On 4 September 2013 22:57, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote: Hi refine bref bonly should be what you are looking for. You may need to use the latest available version (5.8) from our LMB site: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ With best regards Garib On 4 Sep 2013, at 19:59, hari jayaram wrote: Hi, How does one only refine Bs in refmac without changing the model coordinates . Is this accomplished using a zero cycle refinement with b-refinement set. I have never had to do this till now and didnt know how to set it up. Thanks Hari 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/
Re: [ccp4bb] Only refine Bs in Refmac?
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
Re: [ccp4bb] Only refine Bs in Refmac?
Hi Bill, I will add it tomorrow. However with new ccp4 release source code update should be straightforward (I hope). Regards Garib On 5 Sep 2013, at 15:15, William G. Scott 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/
Re: [ccp4bb] Only refine Bs in Refmac?
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/
Re: [ccp4bb] Only refine Bs in Refmac?
Hi Garib, Thanks for your help. I read the document at this locationhttp://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html . 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.ukwrote: 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.eduwrote: 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/
Re: [ccp4bb] Only refine Bs in Refmac?
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/
Re: [ccp4bb] Only refine Bs in Refmac?
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
[ccp4bb] Only refine Bs in Refmac?
Hi, How does one only refine Bs in refmac without changing the model coordinates . Is this accomplished using a zero cycle refinement with b-refinement set. I have never had to do this till now and didnt know how to set it up. Thanks Hari
Re: [ccp4bb] Only refine Bs in Refmac?
Hi refine bref bonly should be what you are looking for. You may need to use the latest available version (5.8) from our LMB site: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ With best regards Garib On 4 Sep 2013, at 19:59, hari jayaram wrote: Hi, How does one only refine Bs in refmac without changing the model coordinates . Is this accomplished using a zero cycle refinement with b-refinement set. I have never had to do this till now and didnt know how to set it up. Thanks Hari 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/
