[ccp4bb] Phaser job on CCP4 suite

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

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Date: 2008-12-03

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From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2008-12-03

Subject: Phaser job on CCP4 suite
From: wangsa tirta ismaya wangsatirta {- at -} GMAIL {- dot -} COM
Date: 2008-12-03

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

--
Wangsa Tirta Ismaya
=====================================
Josef-Israelstraat 66, 9718 GN Groningen
The Netherlands

CCP4bb navigation

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

Previous message:
Subject: Re: Fwd: site mutation evaluation
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-03

Next message:
Subject: tortion angle restraints in REFMAC
From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2008-12-03