[phenixbb] Multiple conformations

Dorothee Liebschner dcliebschner at lbl.gov
Thu Feb 25 10:27:29 PST 2016

Dear all,

To those who are interested in the phenix.polder tool:

An "official" announcement and a detailed description on how to run
phenix.polder will come soon. However, here is some more information for
those who already want to try the tool.

Polder calculates omit maps by excluding the bulk solvent mask to flood
into the area of the atom selection. So they might be effective for atom
selections in binding pockets and around the surface of the protein. Atom
selection can be f.ex. a ligand or a protein residue.

How to run:        phenix.polder model.pdb data.mtz selection="chain A and
resseq 123"

The selection should be one ligand or one residue. I do not recommend
choosing a very large selection, such as several ligands or large number of
residues at once.

To look at the map, open "polder_map_coeffs.mtz" (which has been created by
polder) in COOT, using the "Open MTZ, mmCIF, fcf or phs" option, and by
checking the box "Is a difference map". Then choose map coefficients "mFo-
DFc_polder" and corresponding phases.
If you want to compare to an omit map which has been calculated by deleting
the atom selection from the model, open "mFo-DFc_omit".

Let me know if you have questions.

Best wishes,


On Thu, Feb 25, 2016 at 9:09 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Huanwang,
> it needs to contain diffraction data, Fobs (Iobs) and (optionally) free-r
> flags.
> Pavel
> On 2/25/16 08:55, Huanwang Yang wrote:
>> Dear Pavel,
>> Thanks you so much for the new tool which will be useful to the density
>> validation.
>> I have a question about the mtz file that is provided to the
>> phenix.polder.
>> 1. Does it have to contain the map coefficients such as FOFCWT/PHFOFCWT?
>> 2. If the mtz must contains the FOFCWT/PHFOFCWT, do you have a simple
>> tool that will calculate the map coefficients using your bulk solvent
>> method?
>> Thanks a lot.
>> Huanwang
>> On 02/25/2016 11:29 AM, Pavel Afonine wrote:
>>> Hi Alex,
>>> This is not exactly phenix specific, but I was wondering what are some
>>>> commonly used methods to determine and validate the presence/occurrence of
>>>> multiple conformations for a given amino acid?
>>> I just realized it myself yesterday that most efficient (in terms of
>>> finding answer) way is to use new Phenix tool called phenix.polder (a new
>>> tool being developed in our team in order to better visualize weak
>>> densities in residual Fo-Fc maps), which is available in latest nightly
>>> build. Example:
>>> phenix.polder model.pdb data.mtz selection="chain A and resseq 123"
>>> where "chain A and resseq 123" selects residue in question (this assumes
>>> you have placed one copy of residue conformer).
>>> Pavel
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
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