[phenixbb] Multiple conformations

Huanwang Yang hyang at rcsb.rutgers.edu
Thu Feb 25 08:55:01 PST 2016

Dear Pavel,

Thanks you so much for the new tool which will be useful to the density 

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 

Thanks a lot.


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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