Another possibility is the monomer library. Coot defaults to using
the monomer library installed by CCP4, and CCP4 switched monomer
libraries between 6.1 and 6.2. At least with RNA, Coot relies on its
own internal rules for drawing bonds between residues and only uses the
monomer library for drawing lines within a residue, but its possible
things are different with proteins. You could compare the old MSE
monomer library to the new one and see if anything's changed. The
relevant files are lib/data/monomers/m/MSE.cif file in the old and the
new CCP4 installation directories. Maybe a mean bond length got
shortened, although it seems like something as common as MSE shouldn't
have had any overly dramatic changes.
- Kevin
On 7/23/2011 11:20 AM, Pedro M. Matias wrote:
Hi,
In your PDB file, are the coordinates of the MET residues ATOM or
HETATM lines ?
I suspect HETATM cards in a protein PDB file might have that effect in
COOT.
Cheers,
Pedro.
At 20:43 22-07-2011, Shuilong Tong wrote:
Hi all,
I got broken bonds between MSE and neighboring residues in Coot
0.6.2 under CCP4 6.2.0.
Coot worked well under CCP4 6.1.13, when I updated ccp4 6.1.13 to
6.2.0, the problem raised.
OS info: 64bit OpenSuSE11.3
Could anybody help me ?
Thank you!
shuilong
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___________________________________
Phones : (351-21) 446-9100 Ext. 1669
(351-21) 446-9669 (direct)
Fax : (351-21) 441-1277 or 443-3644
email : [email protected]
http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal
