[buster-discuss] Refining hydrogen atoms

[Wei-Chun Kao]

Dear BUSTER developers,

I am refining a few similar structures ranging from 1.0 to 2.5 Å resolution. I added hydrogen atoms to the models and after refinement, the occupancies of all hydrogen atoms were set to zero. It is clear from refine.log that “All hydrogens are given with zero occupancy, i.e. invisible to X-Ray term”.

I also repeated the 3a4r example in a BUSTER tutorial

https://www.globalphasing.com/buster/wiki/index.cgi?AutobusterHydrogens

with exactly the same commands, except that I needed to use the -full option of “hydrogenate" which is not stated (or was not available then) to keep the occupancies of the existing hydrogen atoms in 3a4r.pdb. After refinement, the occupancies of hydrogen atoms were set to zero, which is perhaps not supposed to be the case in the tutorial?

I got “best refinement in BUSTER reached for FP,SIGFP with R/Rfree 0.2178/0.2291, which are higher than the results shown in the tutorial 0.1982/0.2120. I guess it’s (partly) the effect of excluding hydrogen atoms for refinement?

I have two sets of questions:

1. Is there a way to keep the occupancies of hydrogen atoms to 1.0 for my 1.0-Å resolution dataset? Interestingly the occupancies of all hydrogen atoms in 3a4r.pdb are all 0.88. Is it even sensible to refine the occupancies of hydrogen atoms?

2. For the 2.0-ish Ā resolution datasets, perhaps it is a better idea to set the occupancies of hydrogen atoms to zero? Is this the way BUSTER treats hydrogen atoms as riding model? Will the zero-occupancy hydrogens still improve the geometry of the model at this resolution? 

The BUSTER version is snapshot_20210224, the operating system is CentOS 7.

Best regards,

Wei-Chun

—

Dr. rer. nat. Wei-Chun Kao
wei-chun.kao at biochemie.uni-freiburg.de <mailto:wei-chun.kao at biochemie.uni-freiburg.de>
TEL: +49-761-203-5277 <tel:%2B49-761-203-5277>
orcid.org/0000-0001-8687-6334 <http://orcid.org/0000-0001-8687-6334>						

Institute for Biochemistry and Molecular Biology
AG Carola Hunte
Albert-Ludwigs-Universitaet Freiburg
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D-79104 Freiburg im Breisgau
Germany


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