[phenixbb] How to export difference patterson map in PHENIX

Nathaniel Echols nechols at lbl.gov
Tue Feb 12 06:31:56 PST 2013

On Mon, Feb 11, 2013 at 9:03 AM, 李翔 <lixiang1642 at gmail.com> wrote:
> I got a native and derivative dataset (by soaking) of my crystal and want to
> do MIR in phenix. I am wondering whether there is a way for me to export the
> difference Patterson map so I could have a better idea that whether the
> heavy atom is really in the crystal?

Okay, with a lot of help from Tom Terwilliger, there are two new
commands (starting with build 1296 or newer, hopefully available

cctbx.patterson_map data.mtz

which will generate either a simple or an anomalous Patterson map in
CCP4 format, and:

cctbx.isomorphous_difference_patterson deriv.mtz native.mtz

which does exactly what it sounds like.  Run without arguments or with
"--help" to see a full list of options.

I am not 100% confident that these are entirely correct
implementations - in particular, the anomalous Patterson does not
perfectly agree with the equivalent map from CCP4, I suspect in part
due to different filtering options - but the output is approximately
what we expect.  We will continue testing these when we have a chance
(after we release a new version of Phenix).

One other comment: depending on the heavy atom used and the
wavelength, you may also have anomalous signal, so it's worth checking
for that too - the first tool to try is Xtriage, but you can also look
at the anomalous (single-dataset) Patterson.  (Having never done one
of these experiments, I don't know if there are any good reasons to
use pure MIR phasing, as opposed to MIRAS.)


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