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

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 17 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: 2007-05-17

Next message:
Subject: Re: Refmac5 restrained refinement could not keep the changes made in Turbo
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-18

Subject: Re: MolRep with Phaser using a partial existing solution
From: Tim Grune tim {- dot -} grune {- at -} SYNCHROTRON {- dot -} VIC {- dot -} GOV {- dot -} AU
Date: 2007-05-17

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 <-- 2007 <-- May 2007 <-- 17 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: 2007-05-17