On 23/07/12 22:46, meisam nosrati wrote:
Dear CCP4ers
It seems like the text has not showed up, but I have a problem with
making pdbs from coot. As I refine my structure ( with MR solution )
the beta sheets become loops while H-bondings are still there.
I am not sure, if the problem is originating from making PDBs from coot.
I will appriciate your help
It is not clear to me what the problem is or if there is a problem with
Coot at all.
If you read in the model and write it out again are the beta sheets
still present?
You say "refine" - do you mean you refine with Coot?
Let's presume that you do.
So my guess is that you move the atoms so that they better fit the
density and (quite probably) don't have beta sheet restraints. Thus the
atoms have moved sufficiently so that DSSP (or whatever algorithm you
use to detect SS) no longer recognises those residues as beta strands...
OK...
You want secondary structure to be preserved when you refine with Coot?
Try adding beta strand restraints or initial position restraints or
user-defined inter-strand restraints or use ProSMART's additional bond
restraints.
Paul.
