Dear Phenix developers, I'd like to refine (using phenix.refine) a _very_ incomplete model (obtained by molecular replacement with one subunit of the complete structure) against the native amplitudes, with the goal to obtain meaningful phases and figures_of_merit which should serve to find heavy atom sites in derivative datasets. If I "just refine" in phenix.refine, then the R-factors are in the 50s and the program estimates the coordinate error to be very large. Thus I would like to tell phenix.refine that the coordinates are actually quite accurate, but that a lot of the model is simply missing. I found alpha_beta free_reflections_per_bin= 140 number_of_macromolecule_atoms_absent= 225 n_atoms_included= 0 bf_atoms_absent= 15.0 final_error= 0.0 absent_atom_type= "O" method= *est calc estimation_algorithm= *analytical iterative verbose= -1 interpolation= True fix_scale_for_calc_option= None number_of_waters_absent= 613 sigmaa_estimator kernel_width_free_reflections= 100 kernel_on_chebyshev_nodes= True number_of_sampling_points= 20 number_of_chebyshev_terms= 10 use_sampling_sum_weights= True in the documentation but I have trouble understanding its meanings and defaults - but I do think this should be used. Maybe I should switch to method=calc and specify number_of_macromolecule_atoms_absent= as well as bf_atoms_absent= ? Can anyone advise me, please? thank you, Kay
Hi Kay, the coordinate error is estimated from alpha/beta parameters, and alpha/beta parameters are estimated using test set of Fobs and Fcalc computed from your current model. So, if your model is poor (severely incomplete) then it obviously gets reflected on Fcalc and you get what you get. I guess a way around would be to use an a priori knowledge about the missing structure (amount and location) and incorporate it into alpha and beta but this is not implemented. I played with computing (as opposed to estimation) of alpha and beta (the parameters you refer to below) but it never worked good in my hands, although may be I didn't try hard. I guess it is a nice project to spend a few weeks/a moths on but there is no quick solution right now, sorry. Pavel. On 10/5/10 11:30 AM, Kay Diederichs wrote:
Dear Phenix developers,
I'd like to refine (using phenix.refine) a _very_ incomplete model (obtained by molecular replacement with one subunit of the complete structure) against the native amplitudes, with the goal to obtain meaningful phases and figures_of_merit which should serve to find heavy atom sites in derivative datasets. If I "just refine" in phenix.refine, then the R-factors are in the 50s and the program estimates the coordinate error to be very large. Thus I would like to tell phenix.refine that the coordinates are actually quite accurate, but that a lot of the model is simply missing. I found alpha_beta free_reflections_per_bin= 140 number_of_macromolecule_atoms_absent= 225 n_atoms_included= 0 bf_atoms_absent= 15.0 final_error= 0.0 absent_atom_type= "O" method= *est calc estimation_algorithm= *analytical iterative verbose= -1 interpolation= True fix_scale_for_calc_option= None number_of_waters_absent= 613 sigmaa_estimator kernel_width_free_reflections= 100 kernel_on_chebyshev_nodes= True number_of_sampling_points= 20 number_of_chebyshev_terms= 10 use_sampling_sum_weights= True in the documentation but I have trouble understanding its meanings and defaults - but I do think this should be used. Maybe I should switch to method=calc and specify number_of_macromolecule_atoms_absent= as well as bf_atoms_absent= ?
Can anyone advise me, please?
thank you,
Kay
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Hi Kay I believe incomplete models is one thing the Buster developers claim their program is good at. (Sorry, not a phenix answer.) phx On 06/10/2010 06:08, Pavel Afonine wrote:
Hi Kay,
the coordinate error is estimated from alpha/beta parameters, and alpha/beta parameters are estimated using test set of Fobs and Fcalc computed from your current model. So, if your model is poor (severely incomplete) then it obviously gets reflected on Fcalc and you get what you get.
I guess a way around would be to use an a priori knowledge about the missing structure (amount and location) and incorporate it into alpha and beta but this is not implemented.
I played with computing (as opposed to estimation) of alpha and beta (the parameters you refer to below) but it never worked good in my hands, although may be I didn't try hard.
I guess it is a nice project to spend a few weeks/a moths on but there is no quick solution right now, sorry.
Pavel.
On 10/5/10 11:30 AM, Kay Diederichs wrote:
Dear Phenix developers,
I'd like to refine (using phenix.refine) a _very_ incomplete model (obtained by molecular replacement with one subunit of the complete structure) against the native amplitudes, with the goal to obtain meaningful phases and figures_of_merit which should serve to find heavy atom sites in derivative datasets. If I "just refine" in phenix.refine, then the R-factors are in the 50s and the program estimates the coordinate error to be very large. Thus I would like to tell phenix.refine that the coordinates are actually quite accurate, but that a lot of the model is simply missing. I found alpha_beta free_reflections_per_bin= 140 number_of_macromolecule_atoms_absent= 225 n_atoms_included= 0 bf_atoms_absent= 15.0 final_error= 0.0 absent_atom_type= "O" method= *est calc estimation_algorithm= *analytical iterative verbose= -1 interpolation= True fix_scale_for_calc_option= None number_of_waters_absent= 613 sigmaa_estimator kernel_width_free_reflections= 100 kernel_on_chebyshev_nodes= True number_of_sampling_points= 20 number_of_chebyshev_terms= 10 use_sampling_sum_weights= True in the documentation but I have trouble understanding its meanings and defaults - but I do think this should be used. Maybe I should switch to method=calc and specify number_of_macromolecule_atoms_absent= as well as bf_atoms_absent= ?
Can anyone advise me, please?
thank you,
Kay
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_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Frank von Delft -
Kay Diederichs -
Pavel Afonine