Re: [phenixbb] phenixbb Digest, Vol 78, Issue 9

8 May 2012


      Thank you all. Actually, as Pavel said there is a easy way to do so, I
changed the cif file of the ligand, where I had restraints on the dihedral
modified.


Message: 3
...
Date: Sat, 05 May 2012 13:48:06 -0700
From: Pavel Afonine 
To: [email protected]
Subject: Re: [phenixbb] how to define a molecule in two rigid_body
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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.
Pavel
...
On Sat, May 5, 2012 at 6:39 AM, CPMAS Chen  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
...
...
orientation of these two rings, but there are two concerns that I
...
...
why I did not get the perfect fitting.
1. I might not choose the perfect the orientation of these rings, and
On 5/5/12 10:22 AM, Nathaniel Echols wrote:
the
thought
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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***************************************************

CPMAS Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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