Re: [phenixbb] Please help with neutron composite SA-omit
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
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
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
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
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
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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
Imre Toeroe
-
Pavel Afonine