[phenixbb] how to define a molecule in two rigid_body

Pavel Afonine pafonine at lbl.gov
Sat May 5 13:48:06 PDT 2012

Hi Charles,

I think you are trying to achieve two goals, "keep conformation you 
like" and "make sure it fits given density", while one of the two 
contradicts to the other. That is either the density you are trying to 
fit in your molecule or your expectations about the geometry of the 
molecule (or both) are not quite right.

I think this is how much one can tell given the information you provided.

I don't think you need to do that sophisticated rigid-body kind of 
refinement that you described in your original post. The solution must 
be easier. May be if you send me the model and data and tell which part 
of the model you think is in trouble then probably I could help more.


On 5/5/12 10:22 AM, Nathaniel Echols wrote:
> On Sat, May 5, 2012 at 6:39 AM, CPMAS Chen<cpmasmit at gmail.com>  wrote:
>> I am almost at final stage. but the refinement always shows error density at
>> the single bond connecting the two rings. I have tried manually change the
>> orientation of these two rings, but there are two concerns that I thought
>> why I did not get the perfect fitting.
>> 1. I might not choose the perfect the orientation of these rings, and these
>> give me a non-perfect fitting, and high b-factor.
>> 2. since phenix always tries to change the conformation a little bit to fit
>> the density, so this also might cause some errors, or not the conformation I
>> like.
>> Then, my sense is that, if I can somehow define the two parts of the
>> molecule as two rigid bodies, then phenix only can has free rotation of
>> these two rings, and the fitting might come out good.
> You can define custom planarity restraints for the rings - there isn't
> good documentation for this, but here is what to do:
> 1. If you're using the command line, look here in the .eff file:
> refinement {
>    geometry_restraints {
>      edits {
>        planarity {
>          atom_selection = resseq 1001 and (name C1 or name C2 or name
> C3 or name C4 or name C5 or name C6)
>          sigma = 0.1
>        }
>      }
>    }
> }
> (Other parameters omitted for clarify, of course.  I'm not sure what
> an appropriate sigma would be - you'll probably have to experiment.)
> 2. If you're using the GUI, make sure you have the latest nightly
> build, and on the middle configuration tab, click "Custom geometry
> restraints", which will open a window that includes a tab for creating
> planarity restraints.
> Technically, the two planes won't actually be "rigid bodies" (i.e.
> "constrained"), but if you make the planarity restraint sufficiently
> tight there will be very little deviation from ideality.  (Just don't
> make it too tight, or you'll confuse the minimizer.)
> -Nat
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