Re: [phenixbb] mr problem and changed unit cell parameters

i am using 1.7.1, but i will update it to 1.7.3. i am not sure if the complex has both proteins. Interestingly i am observing this pseudotranslation only in complex structures so i assume that this might be a protein complex with both the proteins. On Tue, Feb 28, 2012 at 12:13 AM, Nathaniel Echols wrote:

On Sun, Feb 26, 2012 at 10:45 PM, intekhab alam wrote:

...

I have collected 2 datasets; one for the native proteins (2.3Å resolution) while other is for a protein-protein complex (3.5Å resolution). The unit cell parameters for the native are a=120, b=196, c=109, a=g=90, b=114, while for the complex data it is a=122, b=197, c=300, a=g=90, b=93. I have successfully got a MR solution and refined the native dataset with 3 monomers in the asymmetric unit. Analysis of the protein complex dataset shows 41% pseudo translation and so far there is no success in molecular replacement for this dataset. Can anyone please suggest me ways to solve this problem. i already have tried different templates like monomer, dimer, trimer, tetramer etc with truncations of loop region. i am using phaser, autoMR, molrep.

Which version are you using? 1.7.3 introduced support for TNCS in Phaser but not AutoMR, but the latest nightly builds have this turned on by default so both programs should be able to handle the problem. (With the minor caveat that the Phaser GUI is broken in dev-991, but hopefully a new build will be available very soon.)

Aside from TNCS, are you certain that your complex really contains both proteins?

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL