Hi Luca,
You should find that the hydrogens in the mmCIF file output by Refmac are
flagged as riding hydrogens, not as an explicit part of the model. This
behaviour is as intended, and should not pose a problem for deposition. They
are not in the output PDB file because there is no way to flag
Hi,
just to clarify one point on the GUI. You can click or unclick the option
"use hydrogens during refinement" on the first tab in i2 GUI in the options
field. As indicated it used it only during refinement and does not put it
into the output pdb. In the output tab you can choose what should
Hello,
just to clarify, I do not use H atoms for refinement, but as idealised riding H
atoms. In the old-style GI of Refmac one could use riding hydrogens during
refinement without adding them in the output coordinate file. I do not find
this option in the new GI of the CCP4i2 window. As a
Dear CCP4 people,
Refining a 1.7 Angstroem structure with REFMAC (CCP4i2) using hydrogens during
refinements by generating riding hydrogens I obtain a PDB file that does not
contain H atoms. However, the corresponding mmcif file that I should use for
deposition contains their coordinates and
