[phenixbb] Calculating map with electron scattering factors

Omar Davulcu davulcuo at ohsu.edu
Tue Feb 10 14:20:49 PST 2015

Hi Pavel,

Thanks for getting back to me.  I'm running Phenix version 1.9, build 1692.  When I run phenix.maps to generate a maps.params file, I don't see electron as an option for scattering_table.  I do see the other four options, though.

When I run phenix.fmodel as you suggested, but substituting the actual name of the pdb file, I get an error message saying:
Sorry: Not a possible choice for scattering_table: electron (command line argument, line 1)
  Possible choices are:

While it seemed pretty straightforward, is it possible that I haven't installed Phenix properly?


From: Pavel Afonine [mailto:pafonine at lbl.gov]
Sent: Tuesday, February 10, 2015 2:07 PM
To: Omar Davulcu; phenixbb at phenix-online.org
Subject: Re: [phenixbb] Calculating map with electron scattering factors

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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