It's in my to-do list to add this option to phenix.maps. Not sure when I will have time to do this though. Conceptually I think that such a trivial exercise as creating an omit map should not require using a such a heavy-duty tool as Autobuild. It can be trivially done using basic low-level cctbx tools. The question is that someone (a Phenix developer) should spend a few moments doing this -:) Pavel On 6/1/12 7:13 AM, Huang, Raven H wrote:

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.

Cheers, Raven

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

On Wed, May 30, 2012 at 11:56 AM, Huang, Raven H wrote: 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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