[phenixbb] phaser output and packing

Matthew Franklin 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
> -- 
> 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
> http://phenix-online.org/mailman/listinfo/phenixbb

Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374

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