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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

------------------------------

-- *************************************************** CPMAS Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************