[phenixbb] Multiple conformations

Pavel Afonine pafonine at lbl.gov
Thu Feb 25 09:09:43 PST 2016

Hi Huanwang,

it needs to contain diffraction data, Fobs (Iobs) and (optionally) 
free-r flags.


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
>> Unsubscribe: phenixbb-leave at phenix-online.org

More information about the phenixbb mailing list