<div class="gmail_quote"><div>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.</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Message: 3<br>
Date: Sat, 05 May 2012 13:48:06 -0700<br>
From: Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>><br>
To: <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
Subject: Re: [phenixbb] how to define a molecule in two rigid_body<br>
Message-ID: <<a href="mailto:4FA59206.7090207@lbl.gov">4FA59206.7090207@lbl.gov</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Hi Charles,<br>
<br>
I think you are trying to achieve two goals, "keep conformation you<br>
like" and "make sure it fits given density", while one of the two<br>
contradicts to the other. That is either the density you are trying to<br>
fit in your molecule or your expectations about the geometry of the<br>
molecule (or both) are not quite right.<br>
<br>
I think this is how much one can tell given the information you provided.<br>
<br>
I don't think you need to do that sophisticated rigid-body kind of<br>
refinement that you described in your original post. The solution must<br>
be easier. May be if you send me the model and data and tell which part<br>
of the model you think is in trouble then probably I could help more.<br>
<br>
Pavel<br>
<br>
On 5/5/12 10:22 AM, Nathaniel Echols wrote:<br>
> On Sat, May 5, 2012 at 6:39 AM, CPMAS Chen<<a href="mailto:cpmasmit@gmail.com">cpmasmit@gmail.com</a>> �wrote:<br>
>> I am almost at final stage. but the refinement always shows error density at<br>
>> the single bond connecting the two rings. I have tried manually change the<br>
>> orientation of these two rings, but there are two concerns that I thought<br>
>> why I did not get the perfect fitting.<br>
>> 1. I might not choose the perfect the orientation of these rings, and these<br>
>> give me a non-perfect fitting, and high b-factor.<br>
>> 2. since phenix always tries to change the conformation a little bit to fit<br>
>> the density, so this also might cause some errors, or not the conformation I<br>
>> like.<br>
>><br>
>> Then, my sense is that, if I can somehow define the two parts of the<br>
>> molecule as two rigid bodies, then phenix only can has free rotation of<br>
>> these two rings, and the fitting might come out good.<br>
> You can define custom planarity restraints for the rings - there isn't<br>
> good documentation for this, but here is what to do:<br>
><br>
> 1. If you're using the command line, look here in the .eff file:<br>
><br>
> refinement {<br>
> � �geometry_restraints {<br>
> � � �edits {<br>
> � � � �planarity {<br>
> � � � � �atom_selection = resseq 1001 and (name C1 or name C2 or name<br>
> C3 or name C4 or name C5 or name C6)<br>
> � � � � �sigma = 0.1<br>
> � � � �}<br>
> � � �}<br>
> � �}<br>
> }<br>
><br>
> (Other parameters omitted for clarify, of course. �I'm not sure what<br>
> an appropriate sigma would be - you'll probably have to experiment.)<br>
><br>
> 2. If you're using the GUI, make sure you have the latest nightly<br>
> build, and on the middle configuration tab, click "Custom geometry<br>
> restraints", which will open a window that includes a tab for creating<br>
> planarity restraints.<br>
><br>
> Technically, the two planes won't actually be "rigid bodies" (i.e.<br>
> "constrained"), but if you make the planarity restraint sufficiently<br>
> tight there will be very little deviation from ideality. �(Just don't<br>
> make it too tight, or you'll confuse the minimizer.)<br>
><br>
> -Nat<br>
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<br>
<br>
<br>
------------------------------<br><br></blockquote></div><div><br></div>-- <br>
<p></p><p>***************************************************</p><p>CPMAS Chen</p><p>Research Associate</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p>
<p></p><br>