reflection file utility and use of modified phases in refinement
Hi everybody, I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)? Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one? Thanks, Engin -- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111
Hi Engin, I'm not sure about your main question...I hope that Nat or Pavel will answer you on that. On the use of density-modified phases in refinement: AutoBuild expects experimental phases in the data file, with experimental HL coefficients, and it by default it will use those HL coefficients in refinement with an MLHL target. The phase probabilities from resolve statistical density modification are pretty accurate, and not inflated, so you could use them in refinement if you wanted to. I don't suggest it, however, because the density-modification phase information is not fully independent of the other information used in refinement (e.g., a flat solvent is implicit in your refinement already, so including that through density modification is partially redundant). ps: I hope AutoBuild doesn't recommend using density-modified phases in refinement, so if you could send me the text where it says that, I will check that out! All the best, Tom T
Hi everybody,
I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)?
Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one?
Thanks,
Engin
-- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Tom, My second question was about autobuild recommending modified phases to be used in further refinement. This is the end of the log file printed by autobuild. See the line for "Data for refinement": Summary of output files for Solution 3 from rebuild cycle 4 --- Model (PDB file) --- pdb_file: AutoBuild_run_1_/cycle_best_4.pdb --- Refinement log file --- log_refine: AutoBuild_run_1_/cycle_best_4.log_refine --- Model-building log file --- log: AutoBuild_run_1_/cycle_best_4.log --- Model-map correlation log file --- log_eval: AutoBuild_run_1_/cycle_best_4.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PH FOFCWT --- refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz --- Density-modification log file --- log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod --- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz If HLAM, HLBM, HLCM and HLDM are density-modified phases, it looks like that's what autobuild suggests. Thanks again, Engin On 8/28/09 7:07 AM, Thomas C. Terwilliger wrote:
Hi Engin,
I'm not sure about your main question...I hope that Nat or Pavel will answer you on that.
On the use of density-modified phases in refinement: AutoBuild expects experimental phases in the data file, with experimental HL coefficients, and it by default it will use those HL coefficients in refinement with an MLHL target.
The phase probabilities from resolve statistical density modification are pretty accurate, and not inflated, so you could use them in refinement if you wanted to. I don't suggest it, however, because the density-modification phase information is not fully independent of the other information used in refinement (e.g., a flat solvent is implicit in your refinement already, so including that through density modification is partially redundant).
ps: I hope AutoBuild doesn't recommend using density-modified phases in refinement, so if you could send me the text where it says that, I will check that out!
All the best, Tom T
Hi everybody,
I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)?
Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one?
Thanks,
Engin
-- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111
_______________________________________________ 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
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Hi Engin, Thanks, yes, I see now what you are looking at: --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz The file exptl_fobs_phases_freeR_flags.mtz has a copy of the (experimental) HL coefficients that were input to autobuild. The labels HLAM HLBM etc are indeed confusing...they have the ending "M" because they were copied by resolve and it outputs HLAM etc...but in fact they are not density modified, just copied straight from the input data file. Thank you for pointing that out. All the best, Tom T
Hi Tom,
My second question was about autobuild recommending modified phases to be used in further refinement. This is the end of the log file printed by autobuild. See the line for "Data for refinement":
Summary of output files for Solution 3 from rebuild cycle 4
--- Model (PDB file) --- pdb_file: AutoBuild_run_1_/cycle_best_4.pdb
--- Refinement log file --- log_refine: AutoBuild_run_1_/cycle_best_4.log_refine
--- Model-building log file --- log: AutoBuild_run_1_/cycle_best_4.log
--- Model-map correlation log file --- log_eval: AutoBuild_run_1_/cycle_best_4.log_eval
--- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PH FOFCWT --- refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz
--- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz
--- Density-modification log file --- log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod
--- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz
If HLAM, HLBM, HLCM and HLDM are density-modified phases, it looks like that's what autobuild suggests.
Thanks again,
Engin
On 8/28/09 7:07 AM, Thomas C. Terwilliger wrote:
Hi Engin,
I'm not sure about your main question...I hope that Nat or Pavel will answer you on that.
On the use of density-modified phases in refinement: AutoBuild expects experimental phases in the data file, with experimental HL coefficients, and it by default it will use those HL coefficients in refinement with an MLHL target.
The phase probabilities from resolve statistical density modification are pretty accurate, and not inflated, so you could use them in refinement if you wanted to. I don't suggest it, however, because the density-modification phase information is not fully independent of the other information used in refinement (e.g., a flat solvent is implicit in your refinement already, so including that through density modification is partially redundant).
ps: I hope AutoBuild doesn't recommend using density-modified phases in refinement, so if you could send me the text where it says that, I will check that out!
All the best, Tom T
Hi everybody,
I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)?
Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one?
Thanks,
Engin
-- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111
_______________________________________________ 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
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Thank you. Another colleague had actually pointed out the issue to me. A detailed explanation of all mtz labels within the documentation might help. Engin On 8/28/09 7:47 AM, Thomas C. Terwilliger wrote:
Hi Engin,
Thanks, yes, I see now what you are looking at:
--- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz
The file exptl_fobs_phases_freeR_flags.mtz has a copy of the (experimental) HL coefficients that were input to autobuild. The labels HLAM HLBM etc are indeed confusing...they have the ending "M" because they were copied by resolve and it outputs HLAM etc...but in fact they are not density modified, just copied straight from the input data file.
Thank you for pointing that out. All the best, Tom T
Hi Tom,
My second question was about autobuild recommending modified phases to be used in further refinement. This is the end of the log file printed by autobuild. See the line for "Data for refinement":
Summary of output files for Solution 3 from rebuild cycle 4
--- Model (PDB file) --- pdb_file: AutoBuild_run_1_/cycle_best_4.pdb
--- Refinement log file --- log_refine: AutoBuild_run_1_/cycle_best_4.log_refine
--- Model-building log file --- log: AutoBuild_run_1_/cycle_best_4.log
--- Model-map correlation log file --- log_eval: AutoBuild_run_1_/cycle_best_4.log_eval
--- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PH FOFCWT --- refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz
--- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz
--- Density-modification log file --- log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod
--- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz
If HLAM, HLBM, HLCM and HLDM are density-modified phases, it looks like that's what autobuild suggests.
Thanks again,
Engin
On 8/28/09 7:07 AM, Thomas C. Terwilliger wrote:
Hi Engin,
I'm not sure about your main question...I hope that Nat or Pavel will answer you on that.
On the use of density-modified phases in refinement: AutoBuild expects experimental phases in the data file, with experimental HL coefficients, and it by default it will use those HL coefficients in refinement with an MLHL target.
The phase probabilities from resolve statistical density modification are pretty accurate, and not inflated, so you could use them in refinement if you wanted to. I don't suggest it, however, because the density-modification phase information is not fully independent of the other information used in refinement (e.g., a flat solvent is implicit in your refinement already, so including that through density modification is partially redundant).
ps: I hope AutoBuild doesn't recommend using density-modified phases in refinement, so if you could send me the text where it says that, I will check that out!
All the best, Tom T
Hi everybody,
I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)?
Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one?
Thanks,
Engin
-- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111
_______________________________________________ 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
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
On Aug 27, 2009, at 8:59 PM, Engin Ozkan wrote:
I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)?
Yes, sorry, it's a bug - I also came across it yesterday trying to do the same thing. Should be fixed in 1.4-151. However, there are several features missing that are required to make handling of R-free flags robust: in particular, if the R-free set is missing reflections for which you have amplitudes, it will not fill these in. Doing this requires refactoring some low-level code - also a high priority for next release, but somewhat complex (since it will also need to deal with flags assigned by thin resolution shells). ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (3)
-
Engin Ozkan -
Nathaniel Echols -
Thomas C. Terwilliger