There were many complaints that Phaser was too strict in its packing check, so since version 2.3 (the one with the soon-to-be-updated version of CCP4), Phaser has by default allowed up to 5% of the trace atoms to clash. In more recent versions (available with Phenix and soon from CCP4), if something is rejected for packing but it otherwise looks like a good potential solution (TFZ>8), then a warning message is triggered and summarised at the end of the logfile.
In our tests the 5% cutoff seems to be a good default, but in cases with low sequence identity (where there are likely to be loops that are very different) we almost always use a tool like our sculptor program or chainsaw in CCP4 to trim off bits that don't align with the target sequence. So I would agree with the suggestion to trim the model. However, in our hands a polyAla model is almost always worse than one where the identical side chains are left intact, and other residues are trimmed at most to the gamma atom. We're always interested in feedback, so if there are still cases where Phaser rejects good solutions we'd like to hear about them! Regards, Randy Read On 1 May 2012, at 00:18, Ho Leung Ng wrote: > When searching for multiple molecules/ASU, you need to be careful with > how the software handles packing. Small but acceptable clashes can > accumulate and cause the searches to fail. I suggest using a highly > trimmed as well as a poly-alanine model. I've had success with both > epmr and Phaser. With Phaser, you'll probably want to loosen the > acceptable number of packing clashes. > > > Ho > > Ho Leung Ng > University of Hawaii at Manoa > Assistant Professor, Department of Chemistry > h...@hawaii.edu > > > On Mon, Apr 30, 2012 at 1:00 PM, CCP4BB automatic digest system > <lists...@jiscmail.ac.uk> wrote: >> Date: Mon, 30 Apr 2012 15:41:54 +0000 >> From: "Ke, Jiyuan" <jiyuan...@vai.org> >> Subject: Suggestions for solving a structure with 8-10 copies per asymmetric >> unit >> >> Dear All, >> >> I have a question regarding solving a crystal structure by molecular >> replacement. It is a single protein with a molecular weight of 25.5 kDa. The >> cell dimension is rather big from the diffraction data ( 90.9 Å, 143.9 Å, >> 216.3Å, 90°, 90°, 90°). The possible space group is P212121. With such a >> big unit cell, we predicted that there are 8-10 molecules per asymmetric >> unit. We have a decent model with sequence similarity of 49%. I tried >> several times with Phaser search with the current model and had difficulty >> to find any clear solution. Has anyone seen such cases and any suggestions >> to solve the structure? Thanks! >> >> Jiyuan Ke, Ph.D. >> Research Scientist >> Van Andel Research Institute >> 333 Bostwick Ave NE >> Grand Rapids, MI 49503 ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
