Hi Anna,
a "kick map" is computed as following: we create a large ensemble of
structures (~500 structures) that are all randomly shaken. The shake
amount (rmsd distortion introduced to coordinates) varies from 0 to
1.0A. Then for each structure the map is computed (mFo-DFc or 2mFo-DFc
or any other requested by the user). And finally, all maps are averaged
out to produce one "averaged kick map".
Obviously, such map is supposed to have less or no bias, less noise, and
potentially can clear up some initially bad densities.
The is currently no paper published about this method; we are preparing
the manuscript. There are scattered references and uses of AK maps,
mostly by Dusan Turk (he originally implemented it in his program MAIN).
Documentation is not yet updated, this is true. Sorry.
In phenix.refine GUI you can just check the corresponding box to compute
a kick map (under map menu).
In command line version you need to supply a parameter file that will
define such map:
refinement.electron_density_maps {
map {
mtz_label_amplitudes = 2FOFCWT
mtz_label_phases = PH2FOFCWT
likelihood_weighted = True
obs_factor = 2
calc_factor = 1
kicked = True
fill_missing_f_obs_with_weighted_f_model = True
}
map {
mtz_label_amplitudes = FOFCWT
mtz_label_phases = PHFOFCWT
likelihood_weighted = True
obs_factor = 1
calc_factor = 1
kicked = True
fill_missing_f_obs_with_weighted_f_model = True
}
}
I was recently trying this with neutron maps and the maps are
significantly better (computed with AK approach).
Please use the latest version of CCI Apps for this.
Let me know if you have any questions or problems.
Pavel.
On 2/24/09 7:58 AM, Anna Gardberg wrote:
Hi, Pavel.
I'm not trying to bring up features, exactly, but rather trying to get
an unbiased, quantitative measure of the the deuterium atoms' nuclear
density. The idea is to compare the visibility of hydrogen or
deuterium atoms with x-ray and neutron diffraction, correlating this
parameter (perhaps in the form of OMIT density) to others.
I have only briefly toyed with kick-maps, but the lack of
documentation (http://phenix-online.org/documentation/refinement.htm
doesn't say much about how best to use them) made it frustrating. Can
you recommend an article about kick maps? Or some suggestions on how
to best use this feature, please?
-Anna
On Mon, Feb 23, 2009 at 11:46 PM, Pavel Afonine <[email protected]> wrote:
Hi Anna,
you can ask phenix.refine produce "kick maps" that are supposed to be less
biased, contain less noise and, if you are lucky, might bring some more
features (that were buried in noise before).
Let me know if you have any questions.
Pavel.
On 2/23/09 11:40 AM, Anna Gardberg wrote:
Hello.
I am attempting to create an SA-omit composite map with neutron
scatterers.
Unfortunately,
phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb"
composite_omit_type=sa_omit scattering_table=neutron
results in an error:
"Sorry, unknown file or keyword: scattering_table=neutron
Possibilities... (use 'phenix.autobuild --help all' to get full help):
general.resolve_pattern_command_list=neutron
density_modification.use_resolve_pattern=neutron
decision_making.semi_acceptable_r=neutron
decision_making.acceptable_r=neutron
multiple_models.multiple_models_starting_resolution=neutron
"
Can someone here help, please?
(For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled
binaries) works on my computer, CNS 1.1 version seems to compile, it
will not run. When I apply the nCNS patch to CNS 1.1, again it seems
to compile, but will not run. )
Regards,
Anna Gardberg
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb