On the interface under Refinement Parameters there are three options 1) Use if present 2) Do not use 3) Generate all
if you are using script then default is generate all (add them riding positions). You can switch to other options: make hydr all # generate all - default option make hydr yes # use if present in the file make hydr no # do not use Controlling output make hout yes # write hydrogens to the output file make hout no # do not write - default optoon I hope it helps regards Garib On 5 Mar 2012, at 19:15, Paul Smith wrote: > Hello CCP4 community, > > I'm posting at large regarding a previously raised issue for REFMAC for which > I cannot find the conclusion in the old threads. > > Specifically, does REFMAC add riding hydrogens during default refinement? > > Though I've not requested that any hydrogens be added, only used if in the > input, I see the following in the output header: > > REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS > > Does anyone know exactly what this remark is referring to? > > Are riding hydrogens added for stereochemical restraints, or are their > scattering contributions calculated regardless of they are explicitly defined? > > Can the hydrogen behavior in REFMAC be more explicitly controlled. > > Thanks, > > --Paul > > Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
