Hi Jay, Maybe try to use the the rhombohedral setting (space group R32:R, with unit cell 229,229,229,81,81,81 ) rather than the hexagonal one used now. Depending on the fft algorithm used to compute structure factors for your partial model, this can save you a chuck off memory/time. You can reindex the data and change the model relatively straightforward reflecting the new set of basis vectors. Cheers Peter Jay Thompson wrote: > The cell is quite big. 300 x 300 x 450 A, 90, 90, 120 (R32). I'm using > the entire resolution range at the moment, but I've just set up another > job with a reduced resolution range. So we'll see how this goes. I > only get this error message when I do a run with Phaser with this > partial known solution fixed. It also does the rotation function fine, > but fails at the translation. Any other suggestions or comments would > be greatly appreciated! Thanks > > Jay > > On 5/17/07, *Tim Grune* <[log in to unmask] > <mailto:[log in to unmask]>> wrote: > > Hi, > > what resolution range do you use? You can try reducing it a little. > How big is your cell? > Tim > > On Friday 18 May 2007 13:46, Jay Thompson wrote: > > Hi, > > > > Thanks for the suggestions and quick reply. Suggestions work great! > > > > But I have another problem and looking back at the ccp4bb, I see that > > Elenor had a similar problem late last year. The error message is as > > follows: > > > > > > <B><FONT COLOR="#FF8800"> > > ---------------------------------- > > OUT OF MEMORY ERROR: St9bad_alloc > > ---------------------------------- > > </FONT></B> > > > > <!--SUMMARY_END--> > > -------------------- > > EXIT STATUS: FAILURE > > -------------------- > > > > CPU Time: 0 days 0 hrs 19 mins 53.80 secs (1193.80 secs) > > Finished: Thu May 17 20:28:14 2007 > > > > </pre> > > </html> > > > > The only suggestion from the ccp4bb threads that I could see was > to try > > running it on a different computer with more memory. I've tried > running > > the job on two different Mac G5 and I get the same error > message. The > > computers that I have are pretty new and have 2 GB of SDRAM. I'm > surprised > > that I have a memory problem. I'm also using the Phaser 1.3.3 (I'm > > assuming this is the latest version). Thanks for all your help, in > > advance. > > > > Jay > > > > On 5/17/07, Jay Thompson <[log in to unmask] > <mailto:[log in to unmask]>> wrote: > > > Hi, > > > > > > I have a question with molecular replacement using Phaser. I'm > trying to > > > solve a complex and I have a partial molecular replacement solution > > > solved using another program. This solution is correct and > makes up ~50% > > > of the entire complex. I wanted to fix this solution and > search for > > > another small fragment of the complex using Phaser. I've been > reading > > > the Phaser manual and it seems that I cannot input a pdb with this > > > partial solution and tell the program to fix this molecule. It > seems > > > that fixed solutions can be only input by putting in its Euler > angles and > > > fractional coordinate > > > translations. Is this correct that I cannot input a pdb and > fix it? If > > > I cannot do this, then is there a quick way to identify the > euler angles > > > and coordinate translations for Phaser. > > > > > > Thanks a lot!! > > > > > > Jay > > -- > Tim Grune > Australian Synchrotron > 800 Blackburn Road > Clayton, VIC 3168 > Australia > >