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*To*: Jan Abendroth <Jan.Abendroth@uni-koeln.de>*Subject*: Re: dm-averaging*From*: Edward Berry <eaberry@lbl.gov>*Date*: Tue, 16 Nov 1999 10:32:32 -0800*CC*: ccp4 <ccp4bb@dl.ac.uk>*Organization*: Lawrence Berkeley Laboratory*References*: <3831A074.EB77C177@uni-koeln.de>*Sender*: owner-ccp4bb@dl.ac.uk

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html *** > once again a question concerning a slightly complicated case of dm and > ncs-averaging. Here's how I understand the problem: 1. Since each of your operators has a transitional (screw?) component, you have no proper symmetry. This means you must use a monomer mask: If mask A covers the dimer and you use it for averaging with operator A1->A2, it will be used also for A2->A1' which is not valid. If there is intimate contact between the dimers then the protein will get mangled a bit by inaccuracies of the mask at the contact. On the other hand the improper symmetry should make determining the monomer mask much easier- NCS correlation will drop sharply outside the correct mask. I think CCP4 has a program to determine NCS masks based on correlation. 2. Since you have 6 monomers you need 6 operators: A1->A1 (1 0 0 0 1 0 0 0 1; 0 0 0) A1->A2 A1->B1 =(A -> B) A1->B2 =(A1->A2)x(A->B) A1->C1 =(A->C) A1->C2 =(A1->A2)x(A->C) Note that the way operator multiplication is usually expressed the order is reversed- if XY goes from x to y and YZ from y to z then XZ = YZ*XY (Multiply the first operator by the second ON THE LEFT) ---- I may be mis-interpreting your "transition component" as a screw component. Any rotation operator whose axis does not pass through the origin will have a translation component. If that translation component is perpendicular to the rotation axis, symmetry will be proper if the rotation is integer-fold (e.g. 2-fold), and the operator A1->A2 will work for A2->A1. In this case you can use a dimer mask, with the same six operators above. Averaging will be two-fold redundant (you average point 1 with point 2 and also point 2 with point 1) but there will be no distortion by a mask border passing between intimate monomers. -- Edward A. Berry, MailStop 3-250 Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley, CA 94720 Phone: +1-510-486-4335 Fax: +1-510-486-6059 Jfax +1-530-323-9836 (you send fax, I receive email) e-mail: EABerry@lbl.gov

**References**:**dm-averaging***From:*Jan Abendroth <Jan.Abendroth@uni-koeln.de>

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