Re: [phenixbb] source of fobs for refinement after AutoSol
Hi James, Yes, that is correct. However if you want...you can just go on to AutoBuild and build a new model from scratch and generate a set of free R flags there, supplying your data as data=mydata.sca. I would recommend this anyway because AutoBuild makes a much better model than AutoSol, and including the model from AutoSol doesn't necessarily help (and can make it worse if the AutoSol model is really incomplete, such as from secondary- structure-only model-building). I use the AutoSol model-building just to see if things are going well and then I throw that model away. This is also the default when you use "after_autosol=True" in AutoBuild and when you run the AutoBuild GUI after running AutoSol. It is convenient to use the data and freeR in in exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to. The key of course is: once you refine a model and want to use that model further...you must use the set of free R flags used in that original refinement from then on. If you throw away that model and start from scratch you can also make a new set of free R flags. The hexdigest REMARK in your PDB file from phenix.refine helps you make sure that this is done correctly. All the best, Tom T On Jul 9, 2009, at 8:35 AM, James Whittle wrote:
Dear Tom:
Ok. Thanks for the quick response!
I should run then run AutoSol again to get this file, and it will have the HL coefficients in it?
--James
On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote:
Hi James,
As you are expecting, in AutoSol the file exptl_fobs_phases_freeR_flags_*.mtz normally contains the experimental Fobs and free R flags for refinement, along with phases and HL coefficients from the experimental phasing.
However if an anisotropy correction is applied to the data, then by default no refinement is done in AutoSol and no exptl_fobs_phases_freeR_flags_*.mtz file is created. This is to ensure that refinement is not carried out against anisotropy- corrected data (you want to refine against the original data, and have phenix.refine apply an anisotropy correction as part of refinement).
If you supply
input_refinement_file=my_data.sca
then my_data.sca will be used for refinement and an exptl_fobs_phases_freeR_flags_*.mtz will be created. Note that my_data.sca can be identical to your input data file if you want. I am guessing that in your case an anisotropy correction was applied to the data in this way.
I hope that helps! -Tom T ps. I am thinking of changing the default to make input_refinement_file automatically defined if an anisotropy correction is applied so that you don't have to do this...
On Jul 9, 2009, at 7:55 AM, whittle wrote:
Dear all,
I have a question regarding the output of AutoSol.
I've run AutoSol, using the data directly from scalepack as a .sca file, and would like to now begin refining the structure I've built.
There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the AutoSol directory. Isn't this the right file to use? Since it's not there, is it proper to use the phaser_2.mtz file for phenix.refine?
--James
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Ok. Good to know that I can do that. I did already try AutoBuild, and found that it got stuck. I also have a partial, 100% identical, molecular replacement model of 1/3 the structure, so I may try giving that to AutoBuild as well to see if it can help. Is there perhaps a means to tell AutoBuild not to re-build the partial model, only to refine it and work on the rest? Thanks for your help! --James On Jul 9, 2009, at 11:12 AM, Tom Terwilliger wrote:
Hi James,
Yes, that is correct.
However if you want...you can just go on to AutoBuild and build a new model from scratch and generate a set of free R flags there, supplying your data as data=mydata.sca. I would recommend this anyway because AutoBuild makes a much better model than AutoSol, and including the model from AutoSol doesn't necessarily help (and can make it worse if the AutoSol model is really incomplete, such as from secondary-structure-only model-building). I use the AutoSol model-building just to see if things are going well and then I throw that model away. This is also the default when you use "after_autosol=True" in AutoBuild and when you run the AutoBuild GUI after running AutoSol. It is convenient to use the data and freeR in in exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to.
The key of course is: once you refine a model and want to use that model further...you must use the set of free R flags used in that original refinement from then on. If you throw away that model and start from scratch you can also make a new set of free R flags. The hexdigest REMARK in your PDB file from phenix.refine helps you make sure that this is done correctly.
All the best, Tom T
On Jul 9, 2009, at 8:35 AM, James Whittle wrote:
Dear Tom:
Ok. Thanks for the quick response!
I should run then run AutoSol again to get this file, and it will have the HL coefficients in it?
--James
On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote:
Hi James,
As you are expecting, in AutoSol the file exptl_fobs_phases_freeR_flags_*.mtz normally contains the experimental Fobs and free R flags for refinement, along with phases and HL coefficients from the experimental phasing.
However if an anisotropy correction is applied to the data, then by default no refinement is done in AutoSol and no exptl_fobs_phases_freeR_flags_*.mtz file is created. This is to ensure that refinement is not carried out against anisotropy- corrected data (you want to refine against the original data, and have phenix.refine apply an anisotropy correction as part of refinement).
If you supply
input_refinement_file=my_data.sca
then my_data.sca will be used for refinement and an exptl_fobs_phases_freeR_flags_*.mtz will be created. Note that my_data.sca can be identical to your input data file if you want. I am guessing that in your case an anisotropy correction was applied to the data in this way.
I hope that helps! -Tom T ps. I am thinking of changing the default to make input_refinement_file automatically defined if an anisotropy correction is applied so that you don't have to do this...
On Jul 9, 2009, at 7:55 AM, whittle wrote:
Dear all,
I have a question regarding the output of AutoSol.
I've run AutoSol, using the data directly from scalepack as a .sca file, and would like to now begin refining the structure I've built.
There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the AutoSol directory. Isn't this the right file to use? Since it's not there, is it proper to use the phaser_2.mtz file for phenix.refine?
--James
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ cbss
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi James, Yes, say: include_input_model=False and it will do just what you said: include_input_model= True The keyword include_input_model defines whether the input model (if any) is to be crossed with models that are derived from it, and the best parts of each kept. It also defines whether the input model is to be included in combination steps during initial model-building. Note that if multiple_models=True and include_input_model=True then no initial cycle of randomization will be carried out and the keyword multiple_models_starting_resolution is ignored. In most cases you should use include_input_model=True If you want to generate maximum diversity with multiple-models then you may wish to use include_input_model=False. Also if you want to decrease the amount of bias from your starting model you may wish to use include_input_model=False. -Tom T On Jul 9, 2009, at 9:31 AM, James Whittle wrote:
Ok. Good to know that I can do that. I did already try AutoBuild, and found that it got stuck.
I also have a partial, 100% identical, molecular replacement model of 1/3 the structure, so I may try giving that to AutoBuild as well to see if it can help.
Is there perhaps a means to tell AutoBuild not to re-build the partial model, only to refine it and work on the rest?
Thanks for your help! --James
On Jul 9, 2009, at 11:12 AM, Tom Terwilliger wrote:
Hi James,
Yes, that is correct.
However if you want...you can just go on to AutoBuild and build a new model from scratch and generate a set of free R flags there, supplying your data as data=mydata.sca. I would recommend this anyway because AutoBuild makes a much better model than AutoSol, and including the model from AutoSol doesn't necessarily help (and can make it worse if the AutoSol model is really incomplete, such as from secondary-structure-only model-building). I use the AutoSol model-building just to see if things are going well and then I throw that model away. This is also the default when you use "after_autosol=True" in AutoBuild and when you run the AutoBuild GUI after running AutoSol. It is convenient to use the data and freeR in in exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to.
The key of course is: once you refine a model and want to use that model further...you must use the set of free R flags used in that original refinement from then on. If you throw away that model and start from scratch you can also make a new set of free R flags. The hexdigest REMARK in your PDB file from phenix.refine helps you make sure that this is done correctly.
All the best, Tom T
On Jul 9, 2009, at 8:35 AM, James Whittle wrote:
Dear Tom:
Ok. Thanks for the quick response!
I should run then run AutoSol again to get this file, and it will have the HL coefficients in it?
--James
On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote:
Hi James,
As you are expecting, in AutoSol the file exptl_fobs_phases_freeR_flags_*.mtz normally contains the experimental Fobs and free R flags for refinement, along with phases and HL coefficients from the experimental phasing.
However if an anisotropy correction is applied to the data, then by default no refinement is done in AutoSol and no exptl_fobs_phases_freeR_flags_*.mtz file is created. This is to ensure that refinement is not carried out against anisotropy- corrected data (you want to refine against the original data, and have phenix.refine apply an anisotropy correction as part of refinement).
If you supply
input_refinement_file=my_data.sca
then my_data.sca will be used for refinement and an exptl_fobs_phases_freeR_flags_*.mtz will be created. Note that my_data.sca can be identical to your input data file if you want. I am guessing that in your case an anisotropy correction was applied to the data in this way.
I hope that helps! -Tom T ps. I am thinking of changing the default to make input_refinement_file automatically defined if an anisotropy correction is applied so that you don't have to do this...
On Jul 9, 2009, at 7:55 AM, whittle wrote:
Dear all,
I have a question regarding the output of AutoSol.
I've run AutoSol, using the data directly from scalepack as a .sca file, and would like to now begin refining the structure I've built.
There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the AutoSol directory. Isn't this the right file to use? Since it's not there, is it proper to use the phaser_2.mtz file for phenix.refine?
--James
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ 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
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Ok. Thank you for pointing me to that. --James On Jul 9, 2009, at 11:33 AM, Tom Terwilliger wrote:
Hi James,
Yes, say:
include_input_model=False
and it will do just what you said:
include_input_model= True The keyword include_input_model defines whether the input model (if any) is to be crossed with models that are derived from it, and the best parts of each kept. It also defines whether the input model is to be included in combination steps during initial model-building. Note that if multiple_models=True and include_input_model=True then no initial cycle of randomization will be carried out and the keyword multiple_models_starting_resolution is ignored. In most cases you should use include_input_model=True If you want to generate maximum diversity with multiple-models then you may wish to use include_input_model=False. Also if you want to decrease the amount of bias from your starting model you may wish to use include_input_model=False. -Tom T
On Jul 9, 2009, at 9:31 AM, James Whittle wrote:
Ok. Good to know that I can do that. I did already try AutoBuild, and found that it got stuck.
I also have a partial, 100% identical, molecular replacement model of 1/3 the structure, so I may try giving that to AutoBuild as well to see if it can help.
Is there perhaps a means to tell AutoBuild not to re-build the partial model, only to refine it and work on the rest?
Thanks for your help! --James
On Jul 9, 2009, at 11:12 AM, Tom Terwilliger wrote:
Hi James,
Yes, that is correct.
However if you want...you can just go on to AutoBuild and build a new model from scratch and generate a set of free R flags there, supplying your data as data=mydata.sca. I would recommend this anyway because AutoBuild makes a much better model than AutoSol, and including the model from AutoSol doesn't necessarily help (and can make it worse if the AutoSol model is really incomplete, such as from secondary-structure-only model-building). I use the AutoSol model-building just to see if things are going well and then I throw that model away. This is also the default when you use "after_autosol=True" in AutoBuild and when you run the AutoBuild GUI after running AutoSol. It is convenient to use the data and freeR in in exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to.
The key of course is: once you refine a model and want to use that model further...you must use the set of free R flags used in that original refinement from then on. If you throw away that model and start from scratch you can also make a new set of free R flags. The hexdigest REMARK in your PDB file from phenix.refine helps you make sure that this is done correctly.
All the best, Tom T
On Jul 9, 2009, at 8:35 AM, James Whittle wrote:
Dear Tom:
Ok. Thanks for the quick response!
I should run then run AutoSol again to get this file, and it will have the HL coefficients in it?
--James
On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote:
Hi James,
As you are expecting, in AutoSol the file exptl_fobs_phases_freeR_flags_*.mtz normally contains the experimental Fobs and free R flags for refinement, along with phases and HL coefficients from the experimental phasing.
However if an anisotropy correction is applied to the data, then by default no refinement is done in AutoSol and no exptl_fobs_phases_freeR_flags_*.mtz file is created. This is to ensure that refinement is not carried out against anisotropy- corrected data (you want to refine against the original data, and have phenix.refine apply an anisotropy correction as part of refinement).
If you supply
input_refinement_file=my_data.sca
then my_data.sca will be used for refinement and an exptl_fobs_phases_freeR_flags_*.mtz will be created. Note that my_data.sca can be identical to your input data file if you want. I am guessing that in your case an anisotropy correction was applied to the data in this way.
I hope that helps! -Tom T ps. I am thinking of changing the default to make input_refinement_file automatically defined if an anisotropy correction is applied so that you don't have to do this...
On Jul 9, 2009, at 7:55 AM, whittle wrote:
Dear all,
I have a question regarding the output of AutoSol.
I've run AutoSol, using the data directly from scalepack as a .sca file, and would like to now begin refining the structure I've built.
There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the AutoSol directory. Isn't this the right file to use? Since it's not there, is it proper to use the phaser_2.mtz file for phenix.refine?
--James
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
_______________________________________________ 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
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ cbss
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
James Whittle -
Tom Terwilliger