Hi
Vineet,
1)
This might work better with Phaser.
2) The interface between the two variable domains and the two
constant domains is more rigid, so you could use two dimers, might improve the
MR signal.
3) In
my memory (but I have not used it) there is an elbow.inp routine in CNS, check
out the documentation.
4)
What is your resolution? Below 2.3 A you could throw your best solution in
ARP/wARP...
Hope
this helps,
Flip
-----Original Message-----Hi,
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Vineet Gaur
Sent: Tuesday, 05 September, 2006 8:27
To: [email protected]
Subject: [ccp4bb]: molecular replacement for Fab molecule
I'm trying to find a molecular replacement solution for a Fab molecule. Have tried a few models with AMoRe. None of them seem to have worked as yet. The best soln. till now has a correlation of 40 and a R factor of 45. I was told that this problem sometimes occurs because of variable elbow angles in the Fab molecules and consequent variable heavy and light chain domain interfaces. So I split my model in to 4 fragments - Light and heavy chains and each chain into variable and constant domains. Now used four models as input (to try n simulate a hetro-tetramer) in AMoRe but the program gets stuck at a stage with the following error message:
'fixed part coming from a 6 body traing output
orientations coming from a 6 body traing output
stop >>o2tndo << no solution selected
stop >> amore<< error in previous step'
would somebody please help me figure this out. Any suggestions to solve the Fab molecular replacement problem in general??
Thanks
