Are you trying to have Coot display the Zn-ligand bonds? That's a
different issue from having refmac recognize and use the metal-ligand
restraints in refinement. (I don't bother to have Coot do this.) Looking
at your environment distances, it looks like refmac has done a
restrained refinement, as your Zn-ligand bond distances look right. You
can tell in the refmac log file if you get a message describing that a
Zn-ligand distance was found and it is not listed as "not be used." (If
you get this latter message, you have the wrong link usage setting
chosen in the CCP4i GUI.) I just had an undergraduate student do the
procedure yesterday to do a restrained refinement for a ZnCys2HisAsp
environment. Refmac picks up the Zn-Cys link in the library without any
intervention, and the Zn-His and Zn-Asp bonds have to be taken care of
in the refmac-generated .cif file. All the links show up in the LINKR
records. There may be a more elegant way to do this but it works.
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 11/9/2012 1:09 PM, SD Y wrote:
Dear All,
Thanks for all the suggestions on low resolution, SG and Zn and I
learned a lot. I am not done yet.
I am trying model co-ordinated ZN+2. I got lot of help from Prof.
Roger Rowlett. Also an excellent protocol is available at
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement. Protocol
seems to be very straight forward. I am not getting the result I wanted.
1. When ever I generate cif file, its not writing any for ZN-SG links
at all.
2. After refmac refinement it only draw in LINK for His-ZN. Please see
the images
https://www.dropbox.com/s/7sl01pcdmxxcu2z/ZN-cpoordination-1.png
https://www.dropbox.com/s/cxlp2m2stbple02/ZN-cpoordination-2.png
3. I get this His-Zn link without using .cif file, so what stage do I
use this .cif file?
4. Though cysteines were placed around 2.2 - 2.5 A from ZN, its not
writing LINK in PDB. I only see
LINKR ZN ZN H 1 SG CYS A
83 ZN-CYS
I dont know what is missing, I also attached the log file which
generated the ZN-His coordination.
Any help is highly appreciated.
Thanks
SDY
------------------------------------------------------------------------
Date: Thu, 8 Nov 2012 14:36:59 +0200
From: mbfro...@post.tau.ac.il
Subject: Re: [ccp4bb] low-resolution and zinc
To: CCP4BB@JISCMAIL.AC.UK
The experiment should be very problematic if I can't determine point
group on the base of the symmetry merging statistics.
Watch CHI2 :-)
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of
Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il <mailto:mbfro...@post.tau.ac.il>
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Nov 8, 2012, at 14:29 , herman.schreu...@sanofi.com
<mailto:herman.schreu...@sanofi.com> wrote:
Then we agree. I got confused because you mentioned"space group"
and not "point group" in your phrase about PHASER and MOLREP and
was afraid others might have gotten confused as well. Also, in
case of twinning or almost crystallographic non-crystallographic
symmetry, determining the point group on the basis of processing
statistics alone can be inconclusive or even misleading. If I
recall correctly, there has recently been a thread about this in
the bulletin board.
Herman
