Hi Paul -
Refmac does indeed add riding hydrogens by default; see here:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/restraints.html#makecif
The REMARK 3 is referring to what you think it is: riding hydrogens have
been added. (They are not, however, written to the output file unless
you request that.)
I believe the H atoms are used for both stereochemistry and scattering,
although there may be some fudging on the scattering factors. Adding
the riding hydrogens generally gives you some improvement in R factors
even with a good quality (i.e. stereochemically correct) model.
If you look at the link I gave above, you will see that you can do three
things with hydrogens: never use them, use the riding hydrogens, or only
use H atoms given in the input file (which you could of course tailor to
your needs).
Hope that helps,
Matt
On 3/5/12 2:15 PM, 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
--
Matthew Franklin, Ph. D.
Senior Research Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(646) 275-7165
