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Hi, Vineet. (If you've got an R factor of 45% already, why not try some rigid body refinement on H1-110, H111-220, L1-110, L111-220 and have a look at the maps? ) Flip Hoedemaeker's suggestion that you split a FAB into dimers is a good one. Here's what I do: 1) From the PDB, select a FAB structure of the same isotype that I'm working with. This gives 99-100% identity on the constant portion and ~60% identity on the variable portion. 2) Take residues 1-110 from chains H and L, save the file as variable.pdb. 2a) Sometimes I cut out the CDRs, especially CDR-H3, since they're unlikely to align well. 3) Take residues 111-220 from chains H and L, save the file as const.pdb. 4) Using MOLREP's ccp4i interface, find the best solution(s) for const.pdb. 5) Fix const_molrep1.pdb and find the best solution(s) for variable.pdb. 6) View the result PDB file in PYMOL or COOT to ensure that the 110-111 transitions are in the right place (modulo symmetry operators). 7) Rigid body refinement, then look at unweighted maps. Good luck! -Anna Gardberg -- Anna S. Gardberg, Ph.D. Postdoctoral Research Associate University of Tennessee On Tue, 5 Sep 2006, Flip Hoedemaeker wrote: >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----- >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 > > >Hi, >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 > > > >
