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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