[phenixbb] phaser output and packing
mfranklin at nysbc.org
Tue Feb 26 10:32:34 PST 2013
Dear Ursula -
(Disclaimer: I usually use phaser in ccp4, and I don't have the latest
version. Not everything I say may be applicable.)
If you're running phaser in the default mode, the packing test looks at
the best (fewest clashes) solution, then screens all other solutions
relative to that. If your best solution has no clashes, then even
solutions below your clash threshold (e.g. 20 clashes) may get filtered
out. I find this behavior annoying, and I explicitly tell phaser to
accept all solutions below X number of clashes.
I'm not sure how to make Phaser do this in Phenix, but I see in the
"Phaser-MR" window that there is an "Other Settings" button; in the
window this pops up, you can try selecting "allow" for the packing
function then "20" for the cutoff. This should work...
Hope that helps,
On 2/25/13 7:39 PM, Ursula Schulze-Gahmen wrote:
> Could somebody explain to me how phaser decides if there is a
> solution. When I look at the log file there are a few solutions in the
> translation function that have fewer than the allowed clashes, but
> they are still not recognized as potential solutions. Why is that. Is
> there another parameter that I should be looking at?
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
> phenixbb mailing list
> phenixbb at phenix-online.org
Matthew Franklin, Ph. D.
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
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