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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
