No subject
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.
-Nat
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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
http://web.mac.com/bosch_lab/
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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> &n=
bsp; unit_cell =3D 191.6999969 191.6999969 311.0539856 90 90 90<=
br> 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> &nbs=
p; 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: =
919-684-5178<br>*******************************************************<br>=
<br><br>On Mon, May 7, 2012 at 12:18 PM, Nathaniel Echols <<a href=3D"ma=
ilto:nechols at lbl.gov">nechols at lbl.gov</a>> wrote:<br><blockquote type=3D=
"cite">On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry <<a href=3D"mailto=
:kddaught at bu.edu">kddaught at bu.edu</a>> 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"> x  =
;y z height &n=
bsp; p-value(height)<br></blockquote></blockquote><blockquote type=3D"cite"=
><blockquote type=3D"cite">( 0.500, 0.500, 0.165 ) : 78.635 (=
6.634e-07)<br></blockquote></blockquote><blockquote type=3D"cite"><blockquo=
te type=3D"cite">( 0.000, 0.000, 0.330 ) : 56.292 (2.795e-05)=
<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote type=3D=
"cite">( 0.500, 0.500, 0.497 ) : 30.920 (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. (I'm not sure w=
hat the<br></blockquote><blockquote type=3D"cite">threshold for this is, bu=
t 80% seems pretty large.) Splitting and<br></blockquote><blockquote =
type=3D"cite">various indexing artifacts can sometimes lead to this. =
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=
type=3D"cite">_______________________________________________<br></blockqu=
ote><blockquote type=3D"cite">phenixbb mailing list<br></blockquote><blockq=
uote type=3D"cite"><a href=3D"mailto:phenixbb at phenix-online.org">phenixbb at p=
henix-online.org</a><br></blockquote><blockquote type=3D"cite"><a href=3D"h=
ttp://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org=
/mailman/listinfo/phenixbb</a><br></blockquote>____________________________=
___________________<br>phenixbb mailing list<br><a href=3D"mailto:phenixbb@=
phenix-online.org">phenixbb at phenix-online.org</a><br>http://phenix-online.o=
rg/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div apple-con=
tent-edited=3D"true">
<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 & 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: +1-410-614-4894<br>Fax: =
+1-410-955-2926<br><a href=3D"http://web.mac.com/bosch_lab/">=
http://web.mac.com/bosch_lab/</a><br><br><br><br></span>
</div>
<br></div></body></html>=
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