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
