Hi Frank and Pascal, I would agree with Frank's point. In general I have been hard-pressed to see significant bias in finished recent structures in the PDB at any resolution. In our paper on iterative-build omit maps I got some help from Gerard Kleywegt to find the structure that we used as an example with significant model bias. All the best, Tom T . >> Óf course, at 1.3A resolution, chances are pretty slim that your

...

structure is riddled with bias -- so you probably will just have to suck it up that part of your ligand is disordered.

(By all means, try these suggestions - but bias things start rearing their head above 2-ish, and it's when you're heading towards 3 that you *seriously* need these tools.) phx

Thomas C. Terwilliger wrote:

...

Hi Pascal,

I think that if you are only concerned about one ligand then there are four overall options. The first, going back before you added the ligand, is likely to be the least biased, then the iterative-build omit, then the SA-omit and kicked maps. The iterative-build omit map is probably the best way to get rid of bias once it has been introduced, but it is also very computationally intensive.

As you are only interested in the ligand, you probably do not need to do a composite map, saving you a lot of time.

So the options are:

1. You can go back to the structure you had just prior to adding that ligand, and simply refine that structure and look carefully at the maps. As the structure has never seen the ligand, you have no worries about bias at all in that map. Of course that map may be from a much earlier stage, so it may not be so clear either...leading to the other options of..

2. Take your current structure and run an SA-omit map or an iterative-build omit map, omitting around a PDB file that you create that contains only the ligand.

3. Or, pretty much equivalent to #2, you can remove your ligand from the structure and just do a run of SA or rebuild-in-place and calculate a map,

4. Or you can calculate a kicked map. For the kicked map, quoting Pavel Afonine:

in your parameter file just add another map scope to the electron_density_maps scope, like this:

electron_density_maps { 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 = False } 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 } }

This will create two additional kick maps in addition to the default maps.

All the best, Tom T

, >> Dear All,I have a theoretical/practical question about omit maps and

...

...

refinement. I am completing the refinement (in Phenix) of a protein-ligand complex at 1.3A resolution. I solved it by MR and automatic rebuilding of the protein alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after TLS and water-picking in Phenix. The model includes everything protein, water, ligand and some ions. However I have some slight doubts one region in my ligand. What would be the best map, less biased, to look at this "very late" stage of the refinement. Are composite or systematic SA omit map useful options at this stage ?

Thanks a lot in advance

Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-825-1013 lab (310)-825-8722 email [email protected] _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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Hi Kendall, could you please try the same command using the latest PHENIX from nightly builds: http://www.phenix-online.org/download/nightly_builds.cgi ? I hope this will solve the problem, but please let me know if not. Pavel. On 9/11/09 7:41 AM, Kendall Nettles wrote:

I got an error in my refinement when I added the map scope below to my refinement parameters file:

Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 86, in run map_manger = refine_object.open_map_files() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 949, in open_map_files return map_manager(refine_object=self) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1151, in __init__ self.map_type_labels.append(self.map_to_str(emap)) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1177, in map_to_str if(abs(emap.obs_factor-int(emap.obs_factor))>1.e-4): TypeError: int() argument must be a string or a number, not 'NoneType'

Any suggestions? I'm still learning the syntax, so I wonder if I missed something? My parameters are listed below.

Best Regards, Kendall Nettles

refinement.main { ordered_solvent=true } refinement.refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ *occupancies \ group_anomalous \ none adp { individual { isotropic = All anisotropic = None }}}

refinement.ncs { find_automatically = False excessive_distance_limit=3 restraint_group { reference = chain A and (resid 306:329 or resid 332:461 or resid 465:526 or resid 533:546 ) selection = chain B and (resid 306:329 or resid 332:461 or resid 465:526 or resid 533:546 )

}

restraint_group { reference = chain C and (resid 306:329 or resid 332:461 or resid 471:526 or resid 533:546 ) selection = chain D and (resid 306:329 or resid 332:461 or resid 471:526 or resid 533:546 ) } }

refinement{ electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None 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 = False } 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 }

}}

On 9/10/09 11:52 PM, "Thomas C. Terwilliger" wrote:

Hi Pascal,

I think that if you are only concerned about one ligand then there are four overall options. The first, going back before you added the ligand, is likely to be the least biased, then the iterative-build omit, then the SA-omit and kicked maps. The iterative-build omit map is probably the best way to get rid of bias once it has been introduced, but it is also very computationally intensive.

As you are only interested in the ligand, you probably do not need to do a composite map, saving you a lot of time.

So the options are:

1. You can go back to the structure you had just prior to adding that ligand, and simply refine that structure and look carefully at the maps. As the structure has never seen the ligand, you have no worries about bias at all in that map. Of course that map may be from a much earlier stage, so it may not be so clear either...leading to the other options of..

2. Take your current structure and run an SA-omit map or an iterative-build omit map, omitting around a PDB file that you create that contains only the ligand.

3. Or, pretty much equivalent to #2, you can remove your ligand from the structure and just do a run of SA or rebuild-in-place and calculate a map,

4. Or you can calculate a kicked map. For the kicked map, quoting Pavel Afonine:

in your parameter file just add another map scope to the electron_density_maps scope, like this:

electron_density_maps { 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 = False } 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 } }

This will create two additional kick maps in addition to the default maps.

All the best, Tom T

, >> Dear All,I have a theoretical/practical question about omit maps and >> refinement. >> I am completing the refinement (in Phenix) of a protein-ligand complex at >> 1.3A resolution. I solved it by MR and automatic rebuilding of the protein >> alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after >> TLS and water-picking in Phenix. The model includes everything protein, >> water, ligand and some ions. >> However I have some slight doubts one region in my ligand. >> What would be the best map, less biased, to look at this "very late" stage >> of the refinement. Are composite or systematic SA omit map useful options >> at this stage ? >> >> Thanks a lot in advance >> >> >> Pascal F. Egea, PhD >> Assistant Professor >> UCLA, David Geffen School of Medicine >> Department of Biological Chemistry >> 314 Biomedical Sciences Research Building >> office (310)-825-1013 >> lab (310)-825-8722 >> email [email protected] >> _______________________________________________ >> phenixbb mailing list >> [email protected] >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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