[buster-discuss] Refining hydrogen atoms

[Wei-Chun Kao]

Dear Clemens,

since the 20210716 snapshot update of BUSTER, the -M HydrogenHybridModel 
option becomes available, so I would like to update some of my previous questions as well.


> On 18. Mar 2021, at 11:04, Clemens Vonrhein <vonrhein at GLOBALPHASING.COM> wrote:
> 
> Dear Wei-Chun,


> One thing to remember after a BUSTER refinement including hydrogens:
> during model validation you might need to tell programs to keep the
> hydrogens as they are and to use the correct (ideal) hydrogen
> position. E.g.
> 
>  molprobity.molprobity keep_hydrogens=True nuclear=False refine.pdb
> 
> if you used the full occupancy, e-cloud model.

In case I have high resolution X-ray data, I use 

aB_hydrogenate -full 

to place hydrogen atoms and refine the coordinates with 

-M HydrogenHybridModel  

Because the hydrogen atoms are refined with full occupancy and are at 
nuclear position, I think there is no need to use 

nuclear=False

but keep_hydrogens=True

right? The validation results from buster-report, molprobity.molprobity
and the wwPDB validation server should be consistent I suppose?


>> Will the
>> zero-occupancy hydrogens still improve the geometry of the model at
>> this resolution?
> 
> Yes: they are fully visible to the geometry term and therefore also to
> the contact term - resulting in better placement of e.g. side-chain
> rotamers etc.

For moderate-resolution data, I first use aB_hydrogenate to add H-atoms 
at zero occupancy and refine the coordinates with BUSTER. If I understood correctly, 
buster-report will first run aB_fix_h_occ to synchronize the occupancy of 
H-atoms from zero to that of the parent atom. If zero-occupancy H-atoms are invisible to
MolProbity (or some of the molprobity executables), how should I use the BUSTER-refined
coordinates for wwPDB validation since similar issues will likely be encountered?

Best,

Wei-Chun


>> The BUSTER version is snapshot_20210224, the operating system is CentOS 7.
> 
> Good.
> 
> If there are further questions regarding BUSTER and hydrogens, please
> let us know!
> 
> Cheers
> 
> Clemens
> 
> [1] https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.3330
> [2] https://journals.iucr.org/d/issues/2018/08/00/mn5114/mn5114fig8.html
> [3] https://www.globalphasing.com/buster/wiki/index.cgi?BusterRvalues
> 
> -- 
> 
> *--------------------------------------------------------------
> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park 
> * Cambridge CB3 0AX, UK                   www.globalphasing.com
> *———————————————————————————————



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.globalphasing.com/pipermail/buster-discuss/attachments/20220107/3e1c0b76/attachment.html>