[phenixbb] phenixbb Digest, Vol 78, Issue 9

CPMAS Chen cpmasmit at gmail.com
Tue May 8 07:24:41 PDT 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 <pafonine at lbl.gov>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] how to define a molecule in two rigid_body
> Message-ID: <4FA59206.7090207 at lbl.gov>
> 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 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
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
> ------------------------------
>
>
-- 

***************************************************

CPMAS Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

******************************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120508/a238208b/attachment-0001.htm>


More information about the phenixbb mailing list