[phenixbb] Using Reference Structure in Phenix Refine

Pavel Afonine pafonine at lbl.gov
Sat Dec 4 21:57:14 PST 2010

  Hi John,

Sorry for the luck of documentation on this matter.
Jeff is the right person to reply to this....

I guess you need to use this to define the relationship between 
reference and your current model atoms:

   reference_model {
     reference_group {
       reference = None
       selection = None

So I presume you do not need to replicate copies in your reference high 
resolution model, but just define the atoms in your current and 
reference model that should approximately match.

If you have any questions or problems then please just send me the input 
files and I will try to figure out the best strategy to use. Or let's 
see what Jeff thinks about it.


On 12/4/10 11:18 AM, John Pascal wrote:
> Hello Everyone,
> I am refining against low resolution data, and I would like to use a
> higher resolution model that is available as a reference structure.
> There are multiple copies of the molecule in the asymmetric unit, each
> with a different chain ID.  Does the reference PDB file need to
> contain multiple copies, such that there is a match for each chain
> (e.g. RESIDs and SEGIDs)?
> Or does phenix figure out that the reference structure refers to
> several copies of the molecule, and you only need a single copy in
> the reference molecule PDB file?  Or will NCS restraints take care of
> this?
> Thanks.
> -John

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