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: 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

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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

Subject: Re: MolRep with Phaser using a partial existing solution
From: Jay Thompson jay {- dot -} xtalman {- at -} GMAIL {- dot -} COM
Date: 2007-05-17

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
>

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