[phenixbb] Please help with neutron composite SA-omit

[Imre Toeroe]

Dear Pavel,

When I follow your suggestion, and set "kicked = True" in the def file
for the  2FOFCWT and FOFCWT section, then at the end of the refinement I
receive an error about duplicate labels, zero length map coefficient and
def file is written to disk. I am using the latest cci_apps. Many thanks
for a suggestion how to solve this problem.

Imre

Pavel Afonine wrote:
> 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 <PAfonine at lbl.gov> 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
>>>> phenixbb at phenix-online.org
>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>>       
>>>>         
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