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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Research Scientist position available
From: STEWART TURLEY turley {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-05-18

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

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

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
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Research Scientist position available
From: STEWART TURLEY turley {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-05-18

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