Multiple conformations
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 am currently refining (for 5 cycles) a pdb with the occupancy of atoms of a specific residue set to 0, and then looking at the difference density map contoured to 3 sigma for extra density. Is this somewhat correct? What else could/should I do? Would using OMIT maps help? (What are OMIT maps, and how do I generate them?) Thanks, Alex (not a crystallographer)
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
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
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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
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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,
Dorothee
On Thu, Feb 25, 2016 at 9:09 AM, Pavel Afonine
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
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participants (4)
-
Alejandro Virrueta -
Dorothee Liebschner -
Huanwang Yang -
Pavel Afonine