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Mon Mar 12 09:43:37 PDT 2012

The full list of Patterson peaks is:

  x      y      z            height   p-value(height)
( 0.500, 0.500, 0.165 ) :   78.635   (6.634e-07)
( 0.000, 0.000, 0.330 ) :   56.292   (2.795e-05)
( 0.500, 0.500, 0.497 ) :   30.920   (1.207e-03)

One word of caution: an exceptionally high off-origin peak can mean
that the unit cell was measured too large, and you've integrated extra
reflections that are really non-existent.  (I'm not sure what the
threshold for this is, but 80% seems pretty large.)  Splitting and
various indexing artifacts can sometimes lead to this.  I'd recommend
running labelit.index on the images and seeing what it thinks the
lattice should be.

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J=FCrgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:      +1-410-614-4894
Fax:      +1-410-955-2926

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<html><head></head><body style=3D"word-wrap: break-word; -webkit-nbsp-mode:=
 space; -webkit-line-break: after-white-space; ">Why don't you index over t=
he whole dataset (XDS) ?<div>Or at least over a couple of images (Mosflm)</=
div><div><br></div><div>J=FCrgen</div><div><br><div><div>On May 7, 2012, at=
 12:50 PM, Kelly Daughtry wrote:</div><br class=3D"Apple-interchange-newlin=
e"><blockquote type=3D"cite"><div>I agree.<br><br>The fact that two "crysta=
ls forms" appear, with related unit cells:<br>P422 data:<br> &nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;unit_cell =3D 191.6999969 191.6999969 311.0539856 90 90 90<=
br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;space_group =3D "P 4 2 2"<br>I422 data:<b=
r>unit_cell =3D 191.783 191.783 103.775 90 90 90<br> &nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;space_group =3D "I 4 2 2"<br><br>indicated to me you have mis-index=
ed the P422 data. It is likely I422.<br>Kelly<br>**************************=
*****************************<br>Kelly Daughtry, Ph.D.<br>Post-Doctoral Fel=
low, Raetz Lab<br>Biochemistry Department<br>Duke University<br>Alex H. San=
ds, Jr. Building<br>303 Research Drive<br>RM 250<br>Durham, NC 27710<br>P: =
<br><br>On Mon, May 7, 2012 at 12:18 PM, Nathaniel Echols &lt;<a href=3D"ma=
ilto:nechols at">nechols at</a>&gt; wrote:<br><blockquote type=3D=
"cite">On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry &lt;<a href=3D"mailto=
:kddaught at">kddaught at</a>&gt; wrote:<br></blockquote><blockquot=
e type=3D"cite"><blockquote type=3D"cite">Looking at the P422 data, it look=
 like you have pseudo translational symmetry.<br></blockquote></blockquote>=
<blockquote type=3D"cite"><blockquote type=3D"cite">Did you try processing =
this data as I422?<br></blockquote></blockquote><blockquote type=3D"cite"><=
blockquote type=3D"cite"><br></blockquote></blockquote><blockquote type=3D"=
cite"><blockquote type=3D"cite">From the P422_xtriage.log:<br></blockquote>=
</blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><br></bloc=
kquote></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite">The=
 full list of Patterson peaks is:<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite"><br></blockquote></blockquote><bloc=
kquote type=3D"cite"><blockquote type=3D"cite">&nbsp; x &nbsp; &nbsp; &nbsp=
;y &nbsp; &nbsp; &nbsp;z &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;height &n=
bsp; p-value(height)<br></blockquote></blockquote><blockquote type=3D"cite"=
><blockquote type=3D"cite">( 0.500, 0.500, 0.165 ) : &nbsp; 78.635 &nbsp; (=
6.634e-07)<br></blockquote></blockquote><blockquote type=3D"cite"><blockquo=
te type=3D"cite">( 0.000, 0.000, 0.330 ) : &nbsp; 56.292 &nbsp; (2.795e-05)=
<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote type=3D=
"cite">( 0.500, 0.500, 0.497 ) : &nbsp; 30.920 &nbsp; (1.207e-03)<br></bloc=
kquote></blockquote><blockquote type=3D"cite"><br></blockquote><blockquote =
type=3D"cite">One word of caution: an exceptionally high off-origin peak ca=
n mean<br></blockquote><blockquote type=3D"cite">that the unit cell was mea=
sured too large, and you've integrated extra<br></blockquote><blockquote ty=
pe=3D"cite">reflections that are really non-existent. &nbsp;(I'm not sure w=
hat the<br></blockquote><blockquote type=3D"cite">threshold for this is, bu=
t 80% seems pretty large.) &nbsp;Splitting and<br></blockquote><blockquote =
type=3D"cite">various indexing artifacts can sometimes lead to this. &nbsp;=
I'd recommend<br></blockquote><blockquote type=3D"cite">running labelit.ind=
ex on the images and seeing what it thinks the<br></blockquote><blockquote =
type=3D"cite">lattice should be.<br></blockquote><blockquote type=3D"cite">=
<br></blockquote><blockquote type=3D"cite">-Nat<br></blockquote><blockquote=
ote><blockquote type=3D"cite">phenixbb mailing list<br></blockquote><blockq=
uote type=3D"cite"><a href=3D"mailto:phenixbb at">phenixbb at p=</a><br></blockquote><blockquote type=3D"cite"><a href=3D"h=
___________________<br>phenixbb mailing list<br><a href=3D"mailto:phenixbb@=">phenixbb at</a><br>http://phenix-online.o=
rg/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div apple-con=
<span class=3D"Apple-style-span" style=3D"border-collapse: separate; color:=
 rgb(0, 0, 0); font-family: Palatino; font-style: normal; font-variant: nor=
mal; font-weight: normal; letter-spacing: normal; line-height: normal; orph=
ans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; w=
hite-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal=
-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decoratio=
ns-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-wid=
th: 0px; font-size: medium; ">......................<br>J=FCrgen Bosch<br>J=
ohns Hopkins University<br>Bloomberg School of Public Health<br>Department =
of Biochemistry &amp; Molecular Biology<br>Johns Hopkins Malaria Research I=
nstitute<br>615 North Wolfe Street, W8708<br>Baltimore, MD 21205<br>Office:=
 +1-410-614-4742<br>Lab: &nbsp; &nbsp; &nbsp;+1-410-614-4894<br>Fax: &nbsp;=
 &nbsp; &nbsp;+1-410-955-2926<br><a href=3D"">=</a><br><br><br><br></span>


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