Can you attach a log file from earlier runs, and one more recent with the less satisfactory restraints
Defaults are buried in the logs but often not easy to find.. Eleanor On 31 January 2018 at 10:40, Maria Håkansson <[email protected]> wrote: > Hi Garib, > > Any news? > > Best regards, > Maria > > Maria Håkansson, PhD, Crystallization Facility Manager > Principal Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > Mobile: +46 (0)76 8585706 <+46%2076%20858%2057%2006> > Web: www.saromics.com > > > > > On 29 Jan 2018, at 19:06, Garib Murshudov <[email protected]> wrote: > > Yes, it should be as simple as this. But first let me test and see what is > the problem. > > Regards > Garib > > > On 29 Jan 2018, at 17:48, Maria Håkansson <[email protected]> > wrote: > > Hi Garib, > > Usually I update from ccp4. > > But I guess if it just to replace the refmac file in the bin directory > under ccp4-7.0 > I think I can manage. Is it so? > > Best, > Maria > > Maria Håkansson, PhD, Crystallization Facility Manager > Principal Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > Mobile: +46 (0)76 8585706 <+46%2076%20858%2057%2006> > Web: www.saromics.com > > > > > On 29 Jan 2018, at 18:43, Garib Murshudov <[email protected]> wrote: > > Thank you. > Do you usually update from ccp4 or you can copy binary file if I send you? > > Regards > Garib > > > On 29 Jan 2018, at 17:42, Maria Håkansson <[email protected]> > wrote: > > Hi Garib, > > It says: Refmac version 5.8.0189 : 21/09/17 > > Best regards, > Maria > > Maria Håkansson, PhD, Crystallization Facility Manager > Principal Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > Mobile: +46 (0)76 8585706 <+46%2076%20858%2057%2006> > Web: www.saromics.com > > > > > On 29 Jan 2018, at 18:40, Garib Murshudov <[email protected]> wrote: > > Hi Maria, > > What is the refmac version? It should be on the top of the log file. > > Regards > Garib > > > On 29 Jan 2018, at 17:03, Maria Håkansson <[email protected]> > wrote: > > Hi, > > I have a question regarding the automatic restraints in Refmac5 and > CCP4Interface 7.0.050. > > For a few years I have relied on automatic restraints settings in the > CCP4I interface which > usually resulted in r.m.s. bond deviations of about 0.02 Å and good > convergence of refinement (lower > R-factors). The last few months this have not been the > case. In structure after structure in different projects we get > consistently r.m.s. deviations of 0.03 Å and more > and lacking or worse convergence. This is not a huge problem since you can > get around it by using user > set weighting terms. Still it is annoying. > > Anyone experiencing the same? > > Best regards, > Maria > > > Maria Håkansson, PhD, Crystallization Facility Manager > Principal Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > Mobile: +46 (0)76 8585706 <+46%2076%20858%2057%2006> > Web: www.saromics.com > > > > > > Dr Garib N Murshudov > MRC-LMB > Francis Crick Avenue > Cambridge > CB2 0QH UK > Web http://www.mrc-lmb.cam.ac.uk, > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > > > > > > Dr Garib N Murshudov > MRC-LMB > Francis Crick Avenue > Cambridge > CB2 0QH UK > Web http://www.mrc-lmb.cam.ac.uk, > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > > > > > > Dr Garib N Murshudov > MRC-LMB > Francis Crick Avenue > Cambridge > CB2 0QH UK > Web http://www.mrc-lmb.cam.ac.uk, > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > > > > >
