Dear Katherine, we used Coot for our work on refining against neutron data with SHELXL-2013 (http://dx.doi.org/10.1107/S1600576713027659) without much problems. Coot correctly displayed D and H atoms and with the corresponding cif-restraints they would not fly about.
As work-around you could use riding hydrogen atoms during refinement (of course, SHELXL uses the correct and temperature dependent inter-nuclei distance for this); if they fly apart, there positions will be recalculated for the next refinement run. The above article also explains to to go from riding hydrogen atoms to refined atoms and contains the corresponding Engh-Huber type restraints for D/H-X distances and angles, and as mentioned above, Coot worked really well for our work. For importing restraints (for neutron data) I recommend the grade server which can include restraints H atoms in cif and in shelxl format. The H-X distance and angle restraints are also nuclei based and hence suitable for use against neutron data. Best, Tim On 05/30/2014 09:09 PM, Katherine Sippel wrote: > Hi all, > > I have been working on a neutron structure and recently discovered an error > in the CCP4 monomer library for deuterated water (DOD). That has been > reported and is being fixed, but in the interim I am trying to make a work > around for importing the monomer. I tried replacing the ccp4 cif with the > restraints from the PDB, but coot fails to connect the atoms. I've tried > downloading the ideal coordinates .sdf file and generating the restraints > that way. I managed to generate a .cif in phenix.elbow. The problem is that > coot seems to think that anything with a "D" atom.type_energy is "N" and if > I change it to "H" then I have to go through and manually change the Hs to > Ds in column 78 before I input it into a refinement program. This is for > Linux (version 0.7.2 distributed with CCP4). I've also tried it with > WinCoot 0.8-pre (revision 5076) since it has it's own monomer library. That > just names everything HOH. > > I've come to terms with the fact that I can't use real space, regularize, > edit chi angles, or edit phi/psi angles. Honestly there is very little > structure tweaking from the X-ray input. I would just like to be able to > not have to choose between disembodied atoms or manually edit my pdb file > before every refinement cycle. Is there a workaround for this issue? > > Thanks for your time, > Katherine > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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