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Re: [ccp4bb] refinement problem of labelled RNA complex
 

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CCP4bb <-- 2008 <-- February 2008 <-- 18 February 2008
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Subject: Re: refinement problem of labelled RNA complex
From: Manish Chandra Pathak pmxtal {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-02-18
Hi,

It's much easier to begin with the cif file created by Refmac5
itself, but this cif file needs to be checked and corrected
manually for the restrains. Certainly, Iodine is not happy
with the current restrains.

Most of the time, i have found problems beginning with the
protonation and the bond order and then extending to the
geometrical freedom of the molecule.

You may want to try Monomer sketcher, where you can manipulate
the monomers visually.

all the best
Manish



-
Center for Advanced Research in Biotechnology
University of Maryland Biotechnology Institute
9600 Gudelsky Drive, Rockville
MD 20850 USA
Tel: +1-240-314-6130; fax: +1-240-314-6255





--- ºîº£·å wrote:

> Dear all;
> I am a fresher of Refmac5. And now I'm trying to refine a protein and labelled RNA complex using
> Refmac. It's a Iodo-U labelled RNA. Unfortunately, these is no appropriate lib file in the
> current refmac dictionaries. So I use cif file which created by Refmc itself, surprisingly, the
> base of uridine distorted greatly. Could someone like to tell me how to make the appropriate cif
> file to solve this problem. Another question is that the RNA has a phosphate group in 5', How
> to define this in the cif file?
>
> Could someone help me? Thanks a lot!
> Best wishes,
>
> Hai-Feng Hou
>
> Biological macromolecule group
> Beijing Synchrotron Radiation Facility
> Institute of High Energy Physics
> Chinese Academy of Sciences
> Beijing, China
> Tel: +86-10-88234208
> E-mail: houhf@ihep.ac.cn
>
> 2008-02-18
>



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