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:
wk1995
it1992
*n_gaussian
neutron
While it seemed
pretty straightforward, is it possible that I haven’t
installed Phenix properly?
Thanks,
Omar
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.
Pavel
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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