[phenixbb] SA omit map

Huang, Raven H huang at illinois.edu
Fri Jun 1 07:13:32 PDT 2012

Hi Nat,

Thanks for the advice. I solved my problem by having a new round of refinement without the ligand, followed by FFT under the Maps in Phenix. A pdb file of the ligand was used to define the size of the calculated map. The map was then used in PyMol for figure preparation. A small map is beneficial so you do not need to read in a big file in Pymol.

I think it is a good idea to add this to FAQ. In publications of protein structures in complex with ligand/substrate/DNA/RNA, it is quite common to cover ligand/substrate/DNA/RNA with the omit map to demonstrate the presence of ligand/substrate/DNA/RNA. Besides, it looks good for the presentation! When people (me included) look for a way to do this in Phenix, they are likely to go Autobuild-create omit map under the Maps in Phenix, which is not what they want.


On May 30, 2012, at 4:11 PM, Nathaniel Echols wrote:

> On Wed, May 30, 2012 at 11:56 AM, Huang, Raven H <huang at illinois.edu> wrote:
>> Was the issue of SA omit map debated last July (involving Tiaard Pining,
>> Pavel, and Folmer) resolved in the newer version of Phenix? Specifically,
>> We'd like to generate the same map for a ligand. It is not for the
>> refinement, but for publication (a reviewer asked us to cover the ligand
>> with the map in a figure).
> After reading over the original thread
> (http://www.phenix-online.org/pipermail/phenixbb/2011-July/017342.html)
> I don't think there was anything to resolve - the issue was a
> misunderstanding about what the output from the omit map calculation
> actually includes.  The MTZ file produced by Phenix will cover the
> entire unit cell, and if you convert this to a CCP4 map, the coverage
> depends on the program settings.  (If you open the map in PyMOL from
> the Phenix GUI, it will cover the entire asymmetric unit plus
> padding.)  If the map type is a 2mFo-DFc map, the interpretable
> density will naturally include the protein.  If it's an mFo-DFc map,
> the ligand should stand out.  In either case, if you want to
> explicitly exclude any non-ligand atoms from the density that appears
> in your figure, you have several options:
> 1. In phenix.refine, you can tell it to output pre-calculated CCP4
> maps covering only an atom selection.  However, I think the result
> will be a box with boundaries defined by the extents of the atom
> selection, which may still include protein atoms.
> 2. phenix.cut_out_density (also in the GUI) does exactly what it
> sounds like; I think this will mask around the atom selection.
> However, it will also shift the extracted density to a P1 box (along
> with the model), which may not be what you want.
> 3. PyMOL probably gives you the greatest amount of control, via the
> isomesh command.
> Personally, I would take the mFo-DFc map from the last refinement
> before you added the ligand, and show that.  Otherwise, just run
> phenix.refine with SA using the ligand-free model, and load the
> mFo-DFc map.  (Unless the reviewer wants the 2mFo-DFc map, but with
> the mFo-DFc map you can usually show just what you're interested in
> without too many tricks.)  I wouldn't spend a huge amount of time
> trying to make the density only cover the ligand with no visual
> artifacts - this can be very misleading and doesn't really make the
> figure any clearer.  (In fact, in at least one case I wished that the
> authors had shown the density for the protein too, because I had no
> way to judge the quality of their ligand density by itself.)
> Maybe this needs to be added to the FAQ list?
> -Nat
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