phaser ep_sad zscore

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Bryan Lepore

8 Dec 2010 8 Dec '10

8:03 p.m.

dev-601 in phaser ep_sad mode, i tried ZSCORE SOLVED 0 to get more sites output, and i can see a peak of about Z=4 in the stdout, but no peaks are written to the .pdb am i applying ZSCORE wrong here? -Bryan

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Nathaniel Echols

8 Dec 8 Dec

8:24 p.m.

On Wed, Dec 8, 2010 at 2:03 PM, Bryan Lepore wrote:

...

dev-601

in phaser ep_sad mode, i tried ZSCORE SOLVED 0 to get more sites output, and i can see a peak of about Z=4 in the stdout, but no peaks are written to the .pdb

am i applying ZSCORE wrong here?

I think this is only used for MR_AUTO mode, i.e. a cutoff for TFZ. -Nat

Bryan Lepore

9:21 p.m.

On Wed, Dec 8, 2010 at 5:24 PM, Nathaniel Echols wrote:

...

I think this is only used for MR_AUTO mode, i.e. a cutoff for TFZ.

and for ep_sad, it appears that Z=6.0 is the lowest score for a site. i take this to mean there is no way to drop the Z-score cutoff in ep_sad mode. -Bryan

Randy Read

9 Dec 9 Dec

7:13 a.m.

Hi, What you need is : LLGCOMPLETE SIGMA <your desired Z-score> See http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#LLGCOMPLETE. Regards, Randy On 8 Dec 2010, at 23:21, Bryan Lepore wrote:

...

On Wed, Dec 8, 2010 at 5:24 PM, Nathaniel Echols wrote:

...
I think this is only used for MR_AUTO mode, i.e. a cutoff for TFZ.

and for ep_sad, it appears that Z=6.0 is the lowest score for a site.

i take this to mean there is no way to drop the Z-score cutoff in ep_sad mode.

-Bryan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Bryan Lepore
Nathaniel Echols
Randy Read