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: [email protected] ----- Original Message ----- From: Dhirendra K Simanshu <[email protected]> Date: Friday, July 17, 2009 5:17 pm Subject: [COOT] Problem in real space refinement for ligand linked to protein. To: [email protected] > 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 >
