[phenixbb] Please help with neutron composite SA-omit

[Pavel Afonine]

Hi Imre,

sorry for the problem. Can you change the label names from

mtz_label_amplitudes = 2FOFCWT
mtz_label_phases = PH2FOFCWT

to, for example:

mtz_label_amplitudes = 2FOFCWT_kick
mtz_label_phases = PH2FOFCWT_kick

for both maps.

Does this help?

Pavel.




On 3/3/09 5:18 AM, Imre Toeroe wrote:
> 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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>>     
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