[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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