Here what you could try: First, make sure your data are not twinned. Second (assuming your data are not twinned), use Self Rotation function (I like GLRF) to determine the exact number of copies in the asu. A search for k=45 should 'show' the existence and orientation of a 8-fold ncs axis. If you don't see anything at k=45, then you don't have 8 copies in the asu. Try different options (e.g. k=60 for 6-fold, k=90 for 4-fold, etc), ultimately k=180 should give you an equal number of 2-fold axes as the number of particles in the asu. Third, try MR with whatever 'geometric' model you have (better smaller then larger). Don't be bothered by low LLG values.If you have a solution that 'makes sense' (packing-wise) compute self rotation functions with Icalc and compare them to those calculated with Iobs. The two should look alike, if the solution is correct. Fourth, assuming the above have worked, you need to go from a 'geometric' model to a 'physical entity' to calculate phases. Mask you protomer and bootstrap real phases by ncs-averaging density modification (e.g. resolve, dm, etc). Fifth, calculate an averaged map, build/improve your initial model and used Pavel's new real_space_refinemnet module to refine it against the averaged density. Real space refinement has larger radius of convergence that classical rigid/positional refinement and works much better at medium resolution (~4A). Good luck! Gino ****************************************************************************** Gino Cingolani, Ph.D. Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Tel: (215) 503 4573 Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________ From: [email protected] on behalf of Roger Rowlett Sent: Saturday, May 02, 2015 11:50 AM To: mohamed noor Cc: PHENIX user mailing list Subject: Re: [phenixbb] Molecular replacement at low resolution Before giving up, search in all 8 possible P422 space groups, individually if necessary. You may have to relax or eliminate packing restraints to get solutions or partial solutions to inspect. Looking at packing of these solutions may give you some clues about the true number of molecules in the ASU and eliminate dome space groups. Matthews calculations are not terribly reliable for N>2. Treat your 8 as a very rough estimate. If Phaser doesn't work, try EPMR. Ultimately, you may not have sufficient data, but we just solved a difficult data set in P222 point group at 3.4 A with N=6, (Matthews predicted N=8). Looking at packing in Coot suggested a packing problem where a tetramer straddled one of the 2 fold axes. Searching for 3 dimers worked nicely. __________________ Roger Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University On May 2, 2015 11:01 AM, "mohamed noor" mailto:[email protected]> wrote: Dear developers I have a dataset to about 4 A in point group P 4 2 2 (Pointless suggests P 41 21 2). The protein is about 11 kDa and has an identity of about 50 % to my search model. Phaser calculated the eLLG to be about 5, and maybe not surprisingly, it failed even after using Sculptor to prepare the model. It also says that solutions with Z-scores more than 8 were rejected for failing the packing test. Are there any suggestions on getting a solution? Solvent content calculation from Xtriage suggests about 8 copies in the asu. Would this be of any help in MR? Thanks. _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

always check k=180 (2-fold ncs) in addition to whatever high symmetry ncs-axis you think is in your data (e.g. k=45, etc). There's no guarantee it will work. It's an experimental approach to attempt for difficult MR cases. ****************************************************************************** Gino Cingolani, Ph.D. Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Tel: (215) 503 4573 Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: [email protected] on behalf of Engin Özkan Sent: Saturday, May 02, 2015 1:09 PM To: [email protected] Subject: Re: [phenixbb] Molecular replacement at low resolution On 5/2/15 11:18 AM, Gino Cingolani wrote:

If you don't see anything at k=45, then you don't have 8 copies in the asu. While checking self rotation functions is a great idea, I would shy away from such categorical assertions as self rotation functions are not always cleanly interpretable (despite GLRF, which is my favorite as well), and an eight-fold NCS might not be due to an eight-fold rotation: you can have eight molecules with different arrangements (such as two C4 "tetramers") as well as with improper NCS, or through translational NCS as well.

Engin _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.