[phenixbb] Calculating map with electron scattering factors

Pavel Afonine pafonine at lbl.gov
Tue Feb 10 14:24:29 PST 2015


Hi Omar,

this is an old version. For latest features you need to use nightly builds:

http://phenix-online.org/download/nightly_builds.cgi

I added electron scattering table option just a few months ago.

Pavel

On 2/10/15 2:20 PM, Omar Davulcu wrote:
>
> 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
>
> *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.
>
> 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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