[phenixbb] Off-topic: Hydrogen images
Pavel Afonine
pafonine at lbl.gov
Mon Apr 20 15:45:19 PDT 2015
Hi Mohamed,
perhaps you can copy some images from here:
http://phenix-online.org/presentations/latest/2012_afonine_ecm27-final.pdf
and also here
http://journals.iucr.org/d/issues/2010/11/00/dz5209/index.html
Or simply
- get data and model from PDB
phenix.fetch_pdb pdb_code --mtz
- compute maps
phenix.maps model.pdb data.mtz
or
phenix.maps model.pdb data.mtz
if it is neutron data set. You may want to remove H so that you can see
them in residual maps:
phenix.reduce -trim model_with_h.pdb > model_no_h.pdb
- use graphical program of your choice to make a picture (I use Pymol).
Examples above use Phenix command line. All the same can be done using
the GUI.
Pavel
On 4/17/15 2:58 PM, mohamed noor wrote:
> Dear all
>
> I will be presenting about protein crystallography to a group of
> PhD-level physicists and need some images from the community.
>
> Would anyone have high-quality images of density maps that show
> hydrogen atoms at
> 1. high and ultra-high X-ray resolution (say, about 1.2 A to about 0.5 A)
> 2. low or medium X-ray resolution (where H atoms are not visible)
> compared with neutron data (with H). Ideally these images should be
> from the same protein so that I can show the power of complementary
> beam source for the diffraction.
>
> A side question - what is the community's preference to get deuterated
> samples? Is it crystal soaking or growing E. coli in deuterium?
>
> All contributions will be credited. Thanks.
>
>
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