[phenixbb] SA omit map

Pavel Afonine pafonine at lbl.gov
Fri Jun 1 16:28:26 PDT 2012

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 -:)


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:
>> 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list