[phenixbb] Calculating map with electron scattering factors

Pavel Afonine pafonine at lbl.gov
Tue Feb 10 14:06:31 PST 2015

Hi Omar,

electron scattering table is fully supported. In phenix.maps it is

scattering_table = wk1995 it1992 *n_gaussian neutron electron

But if you just want to compute a Fourier map from a PDB file then this 
is more straightforward:

phenix.fmodel model.pdb high_res=2.3 scattering_table=electron

You need to have a reasonably recent version of Phenix for this.


On 2/10/15 1:57 PM, Omar Davulcu wrote:
> Hi, everyone.
> Probably a silly question, but here goes…
> I’m trying to calculate a simulated map around a set of coordinates 
> using the electron scattering table.  Phenix.maps doesn’t appear to 
> allow selection of that particular scattering table.
> I noticed that phenix.refine allows me to select that table and I 
> thought I would set the number of macro cycles to 0 and turn off all 
> the refinement options and produce a map that way.  I thought I would 
> generate the structure factors needed as input with phenix.fmodel, but 
> that also doesn’t allow selection of the electron scattering table.
> So, my (naïve) question is: what am I doing wrong?  Is there a way I 
> can calculate this map in phenix? Any help would be greatly appreciated.
> Thanks much!
> Omar Davulcu
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> phenixbb at phenix-online.org
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