Sa_Omit_map_DNA_low_resolution
Hello, I want to generate a simulated annealing omit map around DNA molecule in my protein-DNA complex for publication. My resolution is very low - 5A. 1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part) from pdb and ran phenix.refine with simulated_annealing=True. But resulted Fo-Fc in the omitted region is very weak. Is it because of the low resolution and because big part of the model was omitted? 2. Next, I wanted to generate a composit_sa_omit map as in this case DNA would be deleted in small portions and the resulted map would give me a map I can use for publication: phenix.autobuild data=inp.mtz model=whole.pdb (contains DNA) maps_only=True (to skip rebuilding) composite_omit_type=sa_omit omit_selection=DNA.pdb (contains only DNA coordinates). But the job runs too long and still it seems like it is doing rebuilding. Is this a correct command and correct action to create a sa_omit map for the DNA in my complex? Thank you a lot for the help, Nick
On Sat, Sep 15, 2012 at 8:10 AM, Mikalai Lapkouski
1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part) from pdb and ran phenix.refine with simulated_annealing=True. But resulted Fo-Fc in the omitted region is very weak. Is it because of the low resolution and because big part of the model was omitted?
This is part of the problem - another possible contributing factor is that the bulk solvent mask will extend into the DNA site, which flattens out the difference density. An alternate way to do this (which should work) is to set the occupancy of the DNA to zero, which will remove any contribution to the scattering, and set the parameter ignore_zero_occupancy_atoms=False, which will prevent the mask from extending into the DNA. (This is basically what AutoBuild's omit map feature does internally.)
2. Next, I wanted to generate a composit_sa_omit map as in this case DNA would be deleted in small portions and the resulted map would give me a map I can use for publication:
phenix.autobuild data=inp.mtz model=whole.pdb (contains DNA) maps_only=True (to skip rebuilding) composite_omit_type=sa_omit omit_selection=DNA.pdb (contains only DNA coordinates). But the job runs too long and still it seems like it is doing rebuilding. Is this a correct command and correct action to create a sa_omit map for the DNA in my complex?
My understanding was that the composite omit map generation always works on the entire structure, not a selection of atoms. -Nat
Hi,
1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part) from pdb and ran phenix.refine with simulated_annealing=True. But resulted Fo-Fc in the omitted region is very weak. Is it because of the low resolution and because big part of the model was omitted? This is part of the problem - another possible contributing factor is that the bulk solvent mask will extend into the DNA site, which flattens out the difference density. An alternate way to do this (which should work) is to set the occupancy of the DNA to zero, which will remove any contribution to the scattering, and set the parameter ignore_zero_occupancy_atoms=False, which will prevent the mask from extending into the DNA.
Yes, that's the trick. We should streamline it somehow. However, removing such a big fraction of atoms at once can't be painless: you can't remove arbitrarily large amount of atoms and expect a useful map after that. May be you should split atoms to omit into fractions (like 1/3 or so), and compute OMIT maps for each one fraction, and then combine resulting maps into one. Pavel
On Sat, Sep 15, 2012 at 1:19 PM, Pavel Afonine
Yes, that's the trick. We should streamline it somehow.
It's not clear to me why that parameter is True - in what other circumstances would we expect to find zero-occupancy atoms? A related question: what happens in phenix.maps when omit.selection is set? Right now, it looks like this simply deletes the selected scatterers from the xray structure object, which I assume means the bulk solvent mask will expand to fill the gap. Wouldn't a better method be to set the occupancies to zero and not ignore them when calculating the mask?
However, removing such a big fraction of atoms at once can't be painless: you can't remove arbitrarily large amount of atoms and expect a useful map after that. May be you should split atoms to omit into fractions (like 1/3 or so), and compute OMIT maps for each one fraction, and then combine resulting maps into one.
It's only about 1/8th of the structure (although those phosphates will contribute a lot), so it shouldn't be too awful. But at this resolution I'm not sure what to expect. -Nat
participants (3)
-
Mikalai Lapkouski -
Nathaniel Echols -
Pavel Afonine