Have you tried using the DNA as your search model? - I have had success this way round - certainly more phasing power than your protein model, I guess. Also, refine with your DNA in place, and your phases/ map should improve - hopefully allowing you to place your protein molecules with ease.
Tony. Sent from my iPhone On 21 Jul 2011, at 12:40, "Hubing Lou" <louhub...@gmail.com<mailto:louhub...@gmail.com>> wrote: I was worried as well with the low TFZ score. Usually successful cases with score >8. I am still puzzled why Phaser and Molrep gave different solutions. Does this mean molecular replacement do not work out in this case so more crystals have to be prepared? A little more information might be helpful to dissolve the problem here. The model I used is a protein-DNA complex. The protein was Chainsaw editted but the DNA sequence was directly borrowed from the original model. Best, Hubing On Thu, Jul 21, 2011 at 3:30 PM, Vellieux Frederic <<mailto:frederic.velli...@ibs.fr>frederic.velli...@ibs.fr<mailto:frederic.velli...@ibs.fr>> wrote: Hi, It's not a bad idea to read the Phaser manual for molecular replacement; see <http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement> http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement Soon after the start, in a table on the right hand side, there is: TFZ score < 5, have I solved it ? No. Hence with a TFZ score of 3.8 you do not have a solution using Phaser. Fred. Hubing Lou wrote: Dear all, I am stuck in a molecular replacement case and looking for advices. I have been working on a protein-DNA complex structure. Data was processed by HKL2000 to 2.6Ang and some of the data statistics are shown below: Space group: P21, Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 Redundancy: 2.8 (2.7) Completeness: 94.8 (93.1) Linear R-fac: 0.051 (0.442) Data quality was checked by Phenix.xtriage and there's no problem. I then prepared a model by Chainsaw. Our protein shares only 30% of sequence similarity with the model, but structurally they are in the same group and almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I then ran Phaser in "automated search" mode and there's a solution with RFZ score 4.8, TFZ score 3.8. The electron density map was not bad with DNA double helix clearly seen. However Refmac5 couldn't get Rfree lower than 50%. I then changed to MolRep, ran "self rotation function" first then used the first 10 peaks for translation search. Again there's a solution but it is different from that from Phaser. I attached a picture here. Checking in coot, the packing is the same. But, the refinement couldn't get Rfree lower than 50%. I have tried to include NCS, TLS refinement in Refmac, both not working. Hope someone out there can help. Thanks very much for your time. Hubing ------------------------------------------------------------------------
