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
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, Matt 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
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-- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
On Tue, Feb 26, 2013 at 10:32 AM, Matthew Franklin
(Disclaimer: I usually use phaser in ccp4, and I don't have the latest version. Not everything I say may be applicable.)
Airlie and I put a fair amount of work into making sure that the defaults in the CCP4 version and the Phenix version should be the same, at least to whatever extent they're using [approximately] the same source revision. (Our nightly builds - official releases included - are always using the very latest code. Not sure what CCP4 does.)
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...
I have to admit, this is very poorly labeled right now. I think your advice is correct, but I have added much better captions and help text for the packing options (in the next build, of course). -Nat
participants (3)
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Matthew Franklin -
Nathaniel Echols -
Ursula Schulze-Gahmen