Dear Phenix users, This might be trivial questions though... 1. When you did phenix.model_vs_data, I see the discrepancy between R/Rfree. 'After applying resolution and sigma cutoffs' seems more accurate one though, could someone explain why it has such-even small though- discrepancy? 2. Also, when you do phenix.polygon, I used to seeing many branches from old version. With my current version(phenix-1.6.1-343), I normally see only 5 branches. Is there any reasons for that? Thanks in advance as always. Young-Jin
On Thu, May 13, 2010 at 10:37 AM, Young-Jin Cho
Dear Phenix users, This might be trivial questions though... 1. When you did phenix.model_vs_data, I see the discrepancy between R/Rfree. 'After applying resolution and sigma cutoffs' seems more accurate one though, could someone explain why it has such-even small though- discrepancy?
Not sure I understand the question - what kind of discrepancy? R-free should always be a little higher than R-work... 2. Also, when you do phenix.polygon, I used to seeing many branches from old
version. With my current version(phenix-1.6.1-343), I normally see only 5 branches. Is there any reasons for that?
Yes, we decided that the additional statistics were potentially too confusing and less appropriate as global measures of structure quality (in particular, k_sol should never have been included). You can still add more if you want by clicking the button labeled "Select statistics for display". PS. You should update to the latest official release - 1.6.1-343 was an unofficial nightly build. (Or better yet, just use the latest nightly build, which has many improvements over 1.6.1.) -Nat
Hi Young-Jin, phenix.model_vs_data: - computes the R-factors using all data available, - extracts the R-factors from PDB file header (if available), - extracts resolution limits as well as sigma cutoffs from PDB file header (if available) and re-computes the R-factors using these cutoffs. This is why you get three sets of Rwork/Rfree. Obviously, they may be different. Please let me know if it's still not clear. Pavel. On 5/13/10 10:37 AM, Young-Jin Cho wrote:
Dear Phenix users, This might be trivial questions though... 1. When you did phenix.model_vs_data, I see the discrepancy between R/Rfree. 'After applying resolution and sigma cutoffs' seems more accurate one though, could someone explain why it has such-even small though- discrepancy?
2. Also, when you do phenix.polygon, I used to seeing many branches from old version. With my current version(phenix-1.6.1-343), I normally see only 5 branches. Is there any reasons for that?
Thanks in advance as always.
Young-Jin _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Pavel, I ran phenix.refine to produce a kicked map after deleting my ligand (to get an omit map). I got an error message. Sorry: Duplicate mtz_label_amplitudes:2FOFCWT Here is part of my .def file: How should I change it? map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None kicked = False fill_missing_f_obs_with_weighted_f_model = True } 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 = False } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False }
Hi Maia, change names of the labels for custom defined maps. For example: map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" 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_kick" mtz_label_phases = "PHFOFCWT_kick" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } Pavel. On 5/13/10 11:26 AM, Maia Cherney wrote:
Hi Pavel, I ran phenix.refine to produce a kicked map after deleting my ligand (to get an omit map). I got an error message. Sorry: Duplicate mtz_label_amplitudes:2FOFCWT
Here is part of my .def file: How should I change it?
map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None kicked = False fill_missing_f_obs_with_weighted_f_model = True } 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 = False } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False }
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Thank you, it worked. Maia Pavel Afonine wrote:
Hi Maia,
change names of the labels for custom defined maps. For example:
map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" 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_kick" mtz_label_phases = "PHFOFCWT_kick" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False }
Pavel.
On 5/13/10 11:26 AM, Maia Cherney wrote:
Hi Pavel, I ran phenix.refine to produce a kicked map after deleting my ligand (to get an omit map). I got an error message. Sorry: Duplicate mtz_label_amplitudes:2FOFCWT
Here is part of my .def file: How should I change it?
map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None kicked = False fill_missing_f_obs_with_weighted_f_model = True } 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 = False } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False }
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(Sorry if you got this twice - my first email didn't see to go through...) Hi Young-Jin, phenix.model_vs_data: - computes the R-factors using all data available, - extracts the R-factors from PDB file header (if available), - extracts resolution limits as well as sigma cutoffs from PDB file header (if available) and re-computes the R-factors using these cutoffs. This is why you get three sets of Rwork/Rfree. Obviously, they may be different. Please let me know if it's still not clear. Pavel. On 5/13/10 10:37 AM, Young-Jin Cho wrote:
Dear Phenix users, This might be trivial questions though... 1. When you did phenix.model_vs_data, I see the discrepancy between R/Rfree. 'After applying resolution and sigma cutoffs' seems more accurate one though, could someone explain why it has such-even small though- discrepancy?
2. Also, when you do phenix.polygon, I used to seeing many branches from old version. With my current version(phenix-1.6.1-343), I normally see only 5 branches. Is there any reasons for that?
Thanks in advance as always.
Young-Jin _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Maia Cherney -
Nathaniel Echols -
Pavel Afonine -
Young-Jin Cho