I guess you would need to include your ligand in the refinement, i.e.
use something which is used e.g. in the spherical refinement:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=COOT&P=R2607
or
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Bernhards_key_bindings_for_coot.py
Hope this helps,
B
***************************************************
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487673
fax: (+46) 08-327626
email: [log in to unmask]
----- Original Message -----
From: Dhirendra K Simanshu <[log in to unmask]>
Date: Friday, July 17, 2009 5:17 pm
Subject: [COOT] Problem in real space refinement for ligand linked to
protein.
To: [log in to unmask]
> Hi everyone,
>
> I am trying to refine a structure which contains acetolysine
> (acetyl group
> attached to Lysine residue) in one of the polypeptide. I have refined
> acetolysine present in peptide using Refmac after adding the link
> information in the ligand cif file. After refinement it has linked
> acetolysine properly to polypeptide and seems to have refined it
> quite well.
> I was trying to do real space refinement for this stretch of
> peptide which
> contains acetplysine in coot. I have read the linked cif file using
> readmonomer library option in coot. However, during real space
> refinement it
> breaks the link and refines it as an indiviual ligand not linked to
> aotheramino acids as it should have been. I was wondering how I can
> refine the
> acetolysine in coot using "real space refinement" without breaking
> it from
> the polypeptide.
>
> Thanks
> Regards
> Simanshu
>
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