Re: [ccp4bb] MolRep with Phaser using a partial existing solution

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CCP4bb <-- 2007 <-- May 2007 <-- 18 May 2007

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Subject: Re: MolRep with Phaser using a partial existing solution
From: Jay Thompson jay {- dot -} xtalman {- at -} GMAIL {- dot -} COM
Date: 2007-05-18

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From: proclus {- at -} GNU-DARWIN {- dot -} ORG proclus {- at -} GNU-DARWIN {- dot -} ORG
Date: 2007-05-18

Subject: Re: MolRep with Phaser using a partial existing solution
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2007-05-18

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*
> > 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:
> >
> >
> >
> > ----------------------------------
> > OUT OF MEMORY ERROR: St9bad_alloc
> > ----------------------------------
> >
> >
> >
> > --------------------
> > 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
> >
> >
> >
> >
> > 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
> > 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
>
>

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CCP4bb <-- 2007 <-- May 2007 <-- 18 May 2007

Previous message:
Subject: Re: MolRep with Phaser using a partial existing solution
From: Jay Thompson jay {- dot -} xtalman {- at -} GMAIL {- dot -} COM
Date: 2007-05-18

Next message:
Subject: Re: [Blue-obelisk] a csd alternative
From: proclus {- at -} GNU-DARWIN {- dot -} ORG proclus {- at -} GNU-DARWIN {- dot -} ORG
Date: 2007-05-18