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
> 
>