[phenixbb] Calculating map with electron scattering factors
davulcuo at ohsu.edu
Tue Feb 10 14:20:49 PST 2015
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
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:
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.
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