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CCP4BB  December 2008

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Subject:

Re: Phaser job on CCP4 suite

From:

"Randy J. Read" <[log in to unmask]>

Reply-To:

Randy J. Read

Date:

Wed, 3 Dec 2008 21:00:31 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (67 lines)

Hi,

I've just double-checked this on my installation (6.0.99e still, but 
shouldn't make a difference), and this command works.

I think that you've ended up with an older version of Phaser coming first 
in your path. The syntax of the PACK command has changed (to allow it to 
behave in a way that more users wanted), and an older version will give 
that error message.

If you're on a Unix machine, typing "which phaser" will tell you which 
phaser executable comes first in your path. It could be an earlier CCP4 
installation, or a very old Phenix installation. (More recent Phenix 
installations avoid this issue by calling the executable phenix.phaser, to 
make the name unique.) Another way to tell is from the version number in 
the program banner. This should be 2.1.4 for the version distributed with 
CCP4 6.1.

If that doesn't solve your problem, you can get in touch directly.

Regards,

Randy Read

On Dec 3 2008, wangsa tirta ismaya wrote:

>Dear all,
>
> We are trying to run phaser (for molecular replacement) with the 
> automated search option. The spacegroup is P21 and there are 4 molecules 
> in the ASU. We fed phaser with 1 molecule and let the program generates 
> the symmetry related molecules and packs them into the ASU. As the model 
> grows larger, we observe there is clash between the molecule. SInce we 
> knew that the molecule was funnily oriented (when we run phaser using the 
> initial model, which is much smaller), we expect this problem may appear. 
> Therefore we tried to lower the clashes distance (default 3.0) or 
> increase the maximum allowed number of clashes (default 10). 
> Unfortunately, the program is terminated with this error: 
> ------------------------------------------------------------------------------------- 
> MODE MR_AUTO HKLIN "/wangsa/building/native.run31.mtz" TITLE rerun phaser 
> COMPOSITION PROTEIN SEQ "/home/wangsa/cmtbr.pir" NUMBER 4 ENSEMBLE 
> ensemble1 &
>    PDBFILE "/wangsa/building/phaser5.P21.modelP21212.A.pdb" &
>    IDENT 100.0
>SEARCH ENSEMBLE ensemble1 &
>    NUMBER 4
>PACK BEST
>
> SYNTAX ERROR: Number not present or not valid 
> -------------------------------------------------------------------------------------
>
> The same problem appeared even when we put the values back to default 
> (max 10 clashes and distance 3.0 A) IF we left the run option setting 
> window open during this faulty run (and just changed the value and 
> clicked run). It went back to normal if we first close the run option 
> setting window (and click rerun to open a new run option setting window).
>
>Has anyone experience the same problem or could this be a bug? we are using
>the CCP4 program suite 6.1.0 (CCP4interface 2.0.3).
>
>Many thanks in advance,
>
>
>
>Wangsa
>
>

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