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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