[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:


and also here


Or simply

- get data and model from PDB
phenix.fetch_pdb pdb_code --mtz

- compute maps
phenix.maps model.pdb data.mtz
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.


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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