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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</o:shapelayout></xml><![endif]--></head><body lang=3DEN-US link=3Dblue vli=
nk=3Dpurple><div class=3DWordSection1><p class=3DMsoNormal><a name=3D"_Mail=
EndCompose"><span style=3D'font-family:"Arial","sans-serif";color:#17375E;m=
so-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>=
Hi </span></a><span style=3D'font-family:"Arial","sans-serif";color:#17375E=
;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%=
'>J=FCrgen, Kelly and Nat,<o:p></o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-=
fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p>&nbsp;</o:p><=
/span></p><p class=3DMsoNormal><span style=3D'font-family:"Arial","sans-ser=
if";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-=
fill-alpha:100.0%'>I tried XDS and MosFilm, they simply cannot index the da=
ta. <o:p></o:p></span></p><p class=3DMsoNormal><span style=3D'font-family:"=
Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso=
-style-textfill-fill-alpha:100.0%'><o:p>&nbsp;</o:p></span></p><p class=3DM=
soNormal><span style=3D'font-family:"Arial","sans-serif";color:#17375E;mso-=
style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>I r=
eprocessed the data yesterday with HKL2000 starting from =A0frame #30 (spli=
tting 1-29, 30-360), I did get it indexed to I4 and refined to very nice x/=
y chi^2 and covering most spots, I then used the index/refinement numbers f=
or the whole data set. it seems that other spots were from a &#8220;nicely&=
#8221; positioned secondary crystal which fooled the program to pick P4 spa=
ce group.<o:p></o:p></span></p><p class=3DMsoNormal><span style=3D'font-fam=
ily:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375=
E;mso-style-textfill-fill-alpha:100.0%'><o:p>&nbsp;</o:p></span></p><p clas=
s=3DMsoNormal><span style=3D'font-family:"Arial","sans-serif";color:#17375E=
;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%=
'>I scaled the data as I4 and I422 to see which one is better. The I4 data =
set, ~95% complete overall, 9.2% R-sym. Xtriage suggested it should have hi=
gher symmetry I422 or twin (-k, -h, -l, almost 50%). MR sent well and best =
SG is I4, 2 mol/ASU, r=A0 and r-free went to about 27% and 32%, but if I us=
ed the twin-law in phenix.refine and ask phenix to generate r-free-flags wi=
th twinning in mind, the numbers went to ~22%=A0 and 27%. =A0<o:p></o:p></s=
pan></p><p class=3DMsoNormal><span style=3D'font-family:"Arial","sans-serif=
";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fi=
ll-alpha:100.0%'><o:p>&nbsp;</o:p></span></p><p class=3DMsoNormal style=3D'=
text-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courier Ne=
w"'>Shell Lower Upper Average=A0=A0=A0=A0=A0 Average=A0=A0=A0=A0 Norm. Line=
ar Square<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace=
:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'> limit=A0=
=A0=A0 Angstrom=A0=A0=A0=A0=A0=A0 I=A0=A0 error=A0=A0 stat. Chi**2=A0 R-fac=
=A0 R-fac<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace=
:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=
=A0=A0 50.00=A0=A0 7.32=A0=A0 440.7=A0=A0=A0=A0 8.8=A0=A0=A0=A0 5.1=A0 1.48=
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=A0=A0=A0=A0=A0=A0 7.32=A0=A0 5.81=A0=A0 167.2=A0=A0=A0=A0 4.2=A0=A0=A0=A0 =
3.2=A0 1.868=A0 0.045=A0 0.048<o:p></o:p></span></p><p class=3DMsoNormal st=
yle=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Cou=
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/p><p class=3DMsoNormal style=3D'text-autospace:none'><span style=3D'font-s=
ize:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 4.62=A0=A0 4.29=A0=
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=A0 4.03=A0=A0 3.83=A0=A0 139.5=A0=A0=A0=A0 5.6=A0=A0=A0=A0 5.0=A0 1.740=A0=
 0.083=A0 0.075<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-aut=
ospace:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=
=A0=A0=A0=A0=A0 3.83=A0=A0 3.66=A0=A0 110.2=A0=A0=A0=A0 5.5=A0=A0=A0=A0 5.1=
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=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courie=
r New"'>=A0=A0=A0=A0=A0=A0 3.66=A0=A0 3.52=A0=A0=A0 92.5=A0=A0=A0=A0 5.6=A0=
=A0=A0=A0 5.3=A0 1.459=A0 0.117=A0 0.101<o:p></o:p></span></p><p class=3DMs=
oNormal style=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-f=
amily:"Courier New"'>=A0=A0=A0=A0=A0=A0 3.52=A0=A0 3.40=A0=A0=A0 76.5=A0=A0=
=A0=A0 5.7=A0=A0=A0=A0 5.4=A0 1.372=A0 0.143=A0 0.124<o:p></o:p></span></p>=
<p class=3DMsoNormal style=3D'text-autospace:none'><span style=3D'font-size=
:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 3.40=A0=A0 3.30=A0=A0=
=A0 59.3=A0=A0=A0=A0 5.7=A0=A0=A0=A0 5.5=A0 1.278=A0 0.179=A0 0.146<o:p></o=
:p></span></p><p class=3DMsoNormal style=3D'text-autospace:none'><span styl=
e=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 3.30=A0=
=A0 3.20=A0=A0=A0 47.3=A0=A0=A0=A0 5.7=A0=A0=A0=A0 5.6=A0 1.161=A0 0.212=A0=
 0.179<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:no=
ne'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=
=A0=A0 3.20=A0=A0 3.12=A0=A0=A0 40.7=A0=A0=A0=A0 5.8=A0=A0=A0=A0 5.7=A0 1.1=
03=A0 0.241=A0 0.201<o:p></o:p></span></p><p class=3DMsoNormal style=3D'tex=
t-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'=
>=A0=A0=A0=A0=A0=A0 3.12=A0=A0 3.04=A0=A0=A0 31.6=A0=A0=A0=A0 5.8=A0=A0=A0=
=A0 5.8=A0 1.057=A0 0.298=A0 0.254<o:p></o:p></span></p><p class=3DMsoNorma=
l style=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-family:=
"Courier New"'>=A0=A0=A0=A0=A0=A0 3.04=A0=A0 2.97=A0=A0=A0 28.9=A0=A0=A0=A0=
 5.9=A0=A0=A0=A0 5.9=A0 1.031=A0 0.331=A0 0.271<o:p></o:p></span></p><p cla=
ss=3DMsoNormal style=3D'text-autospace:none'><span style=3D'font-size:9.0pt=
;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 2.97=A0=A0 2.91=A0=A0=A0 22.=
6=A0=A0=A0=A0 5.9=A0=A0=A0=A0 5.9=A0 0.985=A0 0.400=A0 0.340<o:p></o:p></sp=
an></p><p class=3DMsoNormal style=3D'text-autospace:none'><span style=3D'fo=
nt-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 2.91=A0=A0 2.85=
=A0=A0=A0 19.0=A0=A0=A0=A0 6.0=A0=A0=A0=A0 6.0=A0 0.991=A0 0.484=A0 0.405<o=
:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:none'><spa=
n style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 2.=
85=A0=A0 2.80=A0=A0=A0 17.1=A0=A0=A0=A0 6.1=A0=A0=A0=A0 6.1=A0 0.957=A0 0.5=
18=A0 0.437<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospa=
ce:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=
=A0=A0=A0=A0 2.80=A0=A0 2.75=A0=A0=A0 14.6=A0=A0=A0=A0 6.2=A0=A0=A0=A0 6.2=
=A0 0.908=A0 0.577=A0 0.485<o:p></o:p></span></p><p class=3DMsoNormal style=
=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courie=
r New"'>=A0=A0=A0=A0=A0=A0 2.75=A0=A0 2.70=A0=A0=A0 13.0=A0=A0=A0=A0 6.4=A0=
=A0=A0=A0 6.3=A0 0.931=A0 0.645=A0 0.550<o:p></o:p></span></p><p class=3DMs=
oNormal><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0 All r=
eflections=A0=A0=A0 112.9=A0=A0=A0=A0 5.9=A0=A0=A0=A0 5.3=A0 1.455=A0 0.092=
=A0 0.066</span><span style=3D'font-family:"Arial","sans-serif";color:#1737=
5E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.=
0%'><o:p></o:p></span></p><p class=3DMsoNormal><span style=3D'font-family:"=
Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso=
-style-textfill-fill-alpha:100.0%'><o:p>&nbsp;</o:p></span></p><p class=3DM=
soNormal><span style=3D'font-family:"Arial","sans-serif";color:#17375E;mso-=
style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>The=
 I422 data (below), 1 mol/ASU, r and r-free were </span><span style=3D'font=
-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color:#1=
7375E;mso-style-textfill-fill-alpha:100.0%'>about 27% and 32%.</span><span =
style=3D'font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-=
fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p></o:p></span>=
</p><p class=3DMsoNormal><span style=3D'font-family:"Arial","sans-serif";co=
lor:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-a=
lpha:100.0%'><o:p>&nbsp;</o:p></span></p><p class=3DMsoNormal style=3D'text=
-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=
Shell Lower Upper Average=A0=A0=A0=A0=A0 Average=A0=A0=A0=A0 Norm. Linear S=
quare<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:non=
e'><span style=3D'font-size:9.0pt;font-family:"Courier New"'> limit=A0=A0=
=A0 Angstrom=A0=A0=A0=A0=A0=A0 I=A0=A0 error=A0=A0 stat. Chi**2=A0 R-fac=A0=
 R-fac<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:no=
ne'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=
=A0 50.00=A0=A0 7.32=A0=A0 430.0=A0=A0=A0=A0 8.4=A0=A0=A0=A0 5.0=A0 1.344=
=A0 0.025=A0 0.028<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-=
autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=
=A0=A0=A0=A0=A0=A0 7.32=A0=A0 5.81=A0=A0 163.4=A0=A0=A0=A0 4.0=A0=A0=A0=A0 =
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=A0=A0=A0=A0 3.6=A0 1.694=A0 0.046=A0 0.052<o:p></o:p></span></p><p class=
=3DMsoNormal style=3D'text-autospace:none'><span style=3D'font-size:9.0pt;f=
ont-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 5.08=A0=A0 4.62=A0=A0 231.6=A0=
=A0=A0=A0 5.6=A0=A0=A0=A0 4.3=A0 1.790=A0 0.049=A0 0.053<o:p></o:p></span><=
/p><p class=3DMsoNormal style=3D'text-autospace:none'><span style=3D'font-s=
ize:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 4.62=A0=A0 4.29=A0=
=A0 227.8=A0=A0=A0=A0 5.8=A0=A0=A0=A0 4.5=A0 1.534=A0 0.045=A0 0.043<o:p></=
o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:none'><span sty=
le=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 4.29=A0=
=A0 4.03=A0=A0 161.3=A0=A0=A0=A0 5.0=A0=A0=A0=A0 4.2=A0 1.401=A0 0.055=A0 0=
.052<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:none=
'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=
=A0 4.03=A0=A0 3.83=A0=A0 135.3=A0=A0=A0=A0 5.0=A0=A0=A0=A0 4.4=A0 1.367=A0=
 0.066=A0 0.059<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-aut=
ospace:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=
=A0=A0=A0=A0=A0 3.83=A0=A0 3.66=A0=A0 106.2=A0=A0=A0=A0 4.9=A0=A0=A0=A0 4.4=
=A0 1.302=A0 0.082=A0 0.071<o:p></o:p></span></p><p class=3DMsoNormal style=
=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courie=
r New"'>=A0=A0=A0=A0=A0=A0 3.66=A0=A0 3.52=A0=A0=A0 88.1=A0=A0=A0=A0 4.8=A0=
=A0=A0=A0 4.5=A0 1.253=A0 0.097=A0 0.082<o:p></o:p></span></p><p class=3DMs=
oNormal style=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-f=
amily:"Courier New"'>=A0=A0=A0=A0=A0=A0 3.52=A0=A0 3.40=A0=A0=A0 75.0=A0=A0=
=A0=A0 4.9=A0=A0=A0=A0 4.6=A0 1.193=A0 0.113=A0 0.096<o:p></o:p></span></p>=
<p class=3DMsoNormal style=3D'text-autospace:none'><span style=3D'font-size=
:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 3.40=A0=A0 3.30=A0=A0=
=A0 56.7=A0=A0=A0=A0 4.8=A0=A0=A0=A0 4.6=A0 1.121=A0 0.144=A0 0.115<o:p></o=
:p></span></p><p class=3DMsoNormal style=3D'text-autospace:none'><span styl=
e=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 3.30=A0=
=A0 3.20=A0=A0=A0 44.8=A0=A0=A0=A0 4.8=A0=A0=A0=A0 4.7=A0 1.061=A0 0.172=A0=
 0.141<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:no=
ne'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=
=A0=A0 3.20=A0=A0 3.12=A0=A0=A0 38.0=A0=A0=A0=A0 4.8=A0=A0=A0=A0 4.7=A0 1.0=
11=A0 0.203=A0 0.166<o:p></o:p></span></p><p class=3DMsoNormal style=3D'tex=
t-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'=
>=A0=A0=A0=A0=A0=A0 3.12=A0=A0 3.04=A0=A0=A0 29.1=A0=A0=A0=A0 4.7=A0=A0=A0=
=A0 4.7=A0 1.029=A0 0.253=A0 0.209<o:p></o:p></span></p><p class=3DMsoNorma=
l style=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-family:=
"Courier New"'>=A0=A0=A0=A0=A0=A0 3.04=A0=A0 2.97=A0=A0=A0 27.7=A0=A0=A0=A0=
 4.8=A0=A0=A0=A0 4.8=A0 0.985=A0 0.261=A0 0.209<o:p></o:p></span></p><p cla=
ss=3DMsoNormal style=3D'text-autospace:none'><span style=3D'font-size:9.0pt=
;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 2.97=A0=A0 2.91=A0=A0=A0 21.=
4=A0=A0=A0=A0 4.9=A0=A0=A0=A0 4.8=A0 0.917=A0 0.320=A0 0.266<o:p></o:p></sp=
an></p><p class=3DMsoNormal style=3D'text-autospace:none'><span style=3D'fo=
nt-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 2.91=A0=A0 2.85=
=A0=A0=A0 18.3=A0=A0=A0=A0 4.9=A0=A0=A0=A0 4.8=A0 0.949=A0 0.380=A0 0.316<o=
:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospace:none'><spa=
n style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=A0=A0=A0=A0 2.=
85=A0=A0 2.80=A0=A0=A0 16.1=A0=A0=A0=A0 4.9=A0=A0=A0=A0 4.9=A0 0.955=A0 0.4=
31=A0 0.358<o:p></o:p></span></p><p class=3DMsoNormal style=3D'text-autospa=
ce:none'><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0=A0=
=A0=A0=A0=A0 2.80=A0=A0 2.75=A0=A0=A0 14.2=A0=A0=A0=A0 5.0=A0=A0=A0=A0 5.0=
=A0 0.940=A0 0.483=A0 0.399<o:p></o:p></span></p><p class=3DMsoNormal style=
=3D'text-autospace:none'><span style=3D'font-size:9.0pt;font-family:"Courie=
r New"'>=A0=A0=A0=A0=A0=A0 2.75=A0=A0 2.70=A0=A0=A0 12.6=A0=A0=A0=A0 5.2=A0=
=A0=A0=A0 5.2=A0 0.886=A0 0.536=A0 0.462<o:p></o:p></span></p><p class=3DMs=
oNormal><span style=3D'font-size:9.0pt;font-family:"Courier New"'>=A0 All r=
eflections=A0=A0=A0 110.9=A0=A0=A0=A0 5.1=A0=A0=A0=A0 4.5=A0 1.236=A0 0.076=
=A0 0.054</span><span style=3D'font-size:9.0pt;font-family:"Arial","sans-se=
rif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill=
-fill-alpha:100.0%'><o:p></o:p></span></p><p class=3DMsoNormal><span style=
=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p=
>&nbsp;</o:p></span></p><div><p class=3DMsoNormal><b><span style=3D'font-si=
ze:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p>=
</span></b></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-fa=
mily:"Arial","sans-serif";color:#1F497D'>So my questions are:<o:p></o:p></s=
pan></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-family:"A=
rial","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=3DMs=
oListParagraph style=3D'text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !=
supportLists]><span style=3D'font-size:11.0pt;font-family:"Arial","sans-ser=
if";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-=
fill-alpha:100.0%'><span style=3D'mso-list:Ignore'>1.<span style=3D'font:7.=
0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><s=
pan style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375=
E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0=
%'>Is it really twinned since including twin-law in refinment gave much bet=
ter numbers?<o:p></o:p></span></p><p class=3DMsoListParagraph style=3D'text=
-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style=3D=
'font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-=
textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><span sty=
le=3D'mso-list:Ignore'>2.<span style=3D'font:7.0pt "Times New Roman"'>&nbsp=
;&nbsp;&nbsp; </span></span></span><![endif]><span style=3D'font-size:11.0p=
t;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-co=
lor:#17375E;mso-style-textfill-fill-alpha:100.0%'>When refining with twin-l=
aw, Are the maps by phenix.refine output already &#8220;corrected&#8221; mt=
z/map?</span><span style=3D'font-size:11.0pt;font-family:"Arial","sans-seri=
f";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-f=
ill-alpha:100.0%'><o:p></o:p></span></p><p class=3DMsoListParagraph style=
=3D'text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span =
style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;ms=
o-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'><=
span style=3D'mso-list:Ignore'>3.<span style=3D'font:7.0pt "Times New Roman=
"'>&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span style=3D'font-si=
ze:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-textfill=
-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>If I use </span><=
span style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color:#1737=
5E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.=
0%'>xray_data.r_free_flags.generate=3DTrue, can I write the data mtz out wi=
th the generated r-free-flags so that each round of refinement uses the sam=
e CV set?<o:p></o:p></span></p><p class=3DMsoNormal style=3D'margin-left:.2=
5in'><span style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color=
:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alph=
a:100.0%'><o:p>&nbsp;</o:p></span></p><p class=3DMsoNormal><span style=3D'f=
ont-size:11.0pt;font-family:"Arial","sans-serif";color:#17375E;mso-style-te=
xtfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%'>Thnaks,<o:p=
></o:p></span></p><p class=3DMsoNormal><b><span style=3D'font-size:11.0pt;f=
ont-family:"Arial","sans-serif";color:#17375E;mso-style-textfill-fill-color=
:#17375E;mso-style-textfill-fill-alpha:100.0%'><o:p>&nbsp;</o:p></span></b>=
</p><p class=3DMsoNormal><b><span style=3D'font-size:10.5pt;font-family:"Ar=
ial","sans-serif";color:#1F497D'><o:p>&nbsp;</o:p></span></b></p><p class=
=3DMsoNormal><b><span style=3D'font-size:10.5pt;font-family:"Arial","sans-s=
erif";color:#1F497D'><o:p>&nbsp;</o:p></span></b></p><p class=3DMsoNormal><=
b><span style=3D'font-size:10.5pt;font-family:"Arial","sans-serif";color:#1=
F497D'>Tongqing<o:p></o:p></span></b></p><p class=3DMsoNormal><b><span styl=
e=3D'font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p>=
&nbsp;</o:p></span></b></p><p class=3DMsoNormal><b><span style=3D'font-size=
:10.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Tongqing Zhou, Ph.D=
.<o:p></o:p></span></b></p><p class=3DMsoNormal><span style=3D'font-size:10=
.5pt;font-family:"Arial","sans-serif";color:#1F497D'>Staff Scientist<o:p></=
o:p></span></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-fa=
mily:"Arial","sans-serif";color:#1F497D'>Structural Biology Section<o:p></o=
:p></span></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-fam=
ily:"Arial","sans-serif";color:#1F497D'>Vaccine Research Center, NIAID/NIH<=
o:p></o:p></span></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;f=
ont-family:"Arial","sans-serif";color:#1F497D'>Building 40, Room 4609B<o:p>=
</o:p></span></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-=
family:"Arial","sans-serif";color:#1F497D'>40 Convent Drive, MSC3027<o:p></=
o:p></span></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-fa=
mily:"Arial","sans-serif";color:#1F497D'>Bethesda, MD 20892<o:p></o:p></spa=
n></p><p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-family:"Ari=
al","sans-serif";color:#1F497D'>(301) 594-8710 (Tel)<o:p></o:p></span></p><=
p class=3DMsoNormal><span style=3D'font-size:10.5pt;font-family:"Arial","sa=
ns-serif";color:#1F497D'>(301) 793-0794 (Cell)<o:p></o:p></span></p><p clas=
s=3DMsoNormal><span style=3D'font-size:10.5pt;font-family:"Arial","sans-ser=
if";color:#1F497D'>(301) 480-2658 (Fax)<o:p></o:p></span></p><p class=3DMso=
Normal><span style=3D'font-size:10.5pt;font-family:"Arial","sans-serif";col=
or:#A6A6A6'>***************************************************************=
***************<o:p></o:p></span></p><p class=3DMsoNormal><span style=3D'fo=
nt-size:10.5pt;font-family:"Arial","sans-serif";color:#A6A6A6'>The informat=
ion in this e-mail and any of its attachments is confidential and may conta=
in sensitive information. It should not be used by anyone who is not the or=
iginal intended recipient. If you have received this e-mail in error please=
 inform the sender and delete it from your mailbox or any other storage dev=
ices. National Institute of Allergy and Infectious Diseases shall not accep=
t liability for any statements made that are sender's own and not expressly=
 made on behalf of the NIAID by one of its representatives.<o:p></o:p></spa=
n></p><p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Ari=
al","sans-serif";color:#A6A6A6'>*******************************************=
***********************</span><span style=3D'font-size:11.0pt;font-family:"=
Calibri","sans-serif";color:#A6A6A6'><o:p></o:p></span></p></div><p class=
=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri","sans-se=
rif";color:#1F497D'><o:p>&nbsp;</o:p></span></p><div><div style=3D'border:n=
one;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=3DMs=
oNormal><b><span style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif=
"'>From:</span></b><span style=3D'font-size:10.0pt;font-family:"Tahoma","sa=
ns-serif"'> Bosch, Juergen [mailto:jubosch at jhsph.edu] <br><b>Sent:</b> Mond=
ay, May 07, 2012 1:34 PM<br><b>To:</b> PHENIX user mailing list<br><b>Subje=
ct:</b> Re: [phenixbb] Difficult dataset and refinement--P422? I422?Twinnin=
g?<o:p></o:p></span></p></div></div><p class=3DMsoNormal><o:p>&nbsp;</o:p><=
/p><p class=3DMsoNormal>Why don't you index over the whole dataset (XDS) ?<=
o:p></o:p></p><div><p class=3DMsoNormal>Or at least over a couple of images=
 (Mosflm)<o:p></o:p></p></div><div><p class=3DMsoNormal><o:p>&nbsp;</o:p></=
p></div><div><p class=3DMsoNormal>J=FCrgen<o:p></o:p></p></div><div><p clas=
s=3DMsoNormal><o:p>&nbsp;</o:p></p><div><div><p class=3DMsoNormal>On May 7,=
 2012, at 12:50 PM, Kelly Daughtry wrote:<o:p></o:p></p></div><p class=3DMs=
oNormal><br><br><o:p></o:p></p><div><p class=3DMsoNormal>I agree.<br><br>Th=
e fact that two &quot;crystals forms&quot; appear, with related unit cells:=
<br>P422 data:<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;unit_cell =3D 191.6999969 1=
91.6999969 311.0539856 90 90 90<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;space_grou=
p =3D &quot;P 4 2 2&quot;<br>I422 data:<br>unit_cell =3D 191.783 191.783 10=
3.775 90 90 90<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;space_group =3D &quot;I 4 2=
 2&quot;<br><br>indicated to me you have mis-indexed the P422 data. It is l=
ikely I422.<br>Kelly<br>***************************************************=
****<br>Kelly Daughtry, Ph.D.<br>Post-Doctoral Fellow, Raetz Lab<br>Biochem=
istry Department<br>Duke University<br>Alex H. Sands, Jr. Building<br>303 R=
esearch Drive<br>RM 250<br>Durham, NC 27710<br>P: 919-684-5178<br>*********=
**********************************************<br><br><br>On Mon, May 7, 20=
12 at 12:18 PM, Nathaniel Echols &lt;<a href=3D"mailto:nechols at lbl.gov">nec=
hols at lbl.gov</a>&gt; wrote:<br><br><o:p></o:p></p><p class=3DMsoNormal>On M=
on, May 7, 2012 at 8:46 AM, Kelly Daughtry &lt;<a href=3D"mailto:kddaught at b=
u.edu">kddaught at bu.edu</a>&gt; wrote:<o:p></o:p></p><blockquote style=3D'ma=
rgin-top:5.0pt;margin-bottom:5.0pt'><blockquote style=3D'margin-top:5.0pt;m=
argin-bottom:5.0pt'><p class=3DMsoNormal>Looking at the P422 data, it look =
like you have pseudo translational symmetry.<o:p></o:p></p></blockquote></b=
lockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><block=
quote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal>D=
id you try processing this data as I422?<o:p></o:p></p></blockquote></block=
quote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><blockquot=
e style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal><o:p>=
&nbsp;</o:p></p></blockquote></blockquote><blockquote style=3D'margin-top:5=
.0pt;margin-bottom:5.0pt'><blockquote style=3D'margin-top:5.0pt;margin-bott=
om:5.0pt'><p class=3DMsoNormal>From the P422_xtriage.log:<o:p></o:p></p></b=
lockquote></blockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:=
5.0pt'><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p class=
=3DMsoNormal><o:p>&nbsp;</o:p></p></blockquote></blockquote><blockquote sty=
le=3D'margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style=3D'margin-top=
:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal>The full list of Patterson=
 peaks is:<o:p></o:p></p></blockquote></blockquote><blockquote style=3D'mar=
gin-top:5.0pt;margin-bottom:5.0pt'><blockquote style=3D'margin-top:5.0pt;ma=
rgin-bottom:5.0pt'><p class=3DMsoNormal><o:p>&nbsp;</o:p></p></blockquote><=
/blockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><blo=
ckquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal=
>&nbsp; x &nbsp; &nbsp; &nbsp;y &nbsp; &nbsp; &nbsp;z &nbsp; &nbsp; &nbsp; =
&nbsp; &nbsp; &nbsp;height &nbsp; p-value(height)<o:p></o:p></p></blockquot=
e></blockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><=
blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNor=
mal>( 0.500, 0.500, 0.165 ) : &nbsp; 78.635 &nbsp; (6.634e-07)<o:p></o:p></=
p></blockquote></blockquote><blockquote style=3D'margin-top:5.0pt;margin-bo=
ttom:5.0pt'><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p c=
lass=3DMsoNormal>( 0.000, 0.000, 0.330 ) : &nbsp; 56.292 &nbsp; (2.795e-05)=
<o:p></o:p></p></blockquote></blockquote><blockquote style=3D'margin-top:5.=
0pt;margin-bottom:5.0pt'><blockquote style=3D'margin-top:5.0pt;margin-botto=
m:5.0pt'><p class=3DMsoNormal>( 0.500, 0.500, 0.497 ) : &nbsp; 30.920 &nbsp=
; (1.207e-03)<o:p></o:p></p></blockquote></blockquote><blockquote style=3D'=
margin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal><o:p>&nbsp;</o:p=
></p></blockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt=
'><p class=3DMsoNormal>One word of caution: an exceptionally high off-origi=
n peak can mean<o:p></o:p></p></blockquote><blockquote style=3D'margin-top:=
5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal>that the unit cell was meas=
ured too large, and you've integrated extra<o:p></o:p></p></blockquote><blo=
ckquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal=
>reflections that are really non-existent. &nbsp;(I'm not sure what the<o:p=
></o:p></p></blockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom=
:5.0pt'><p class=3DMsoNormal>threshold for this is, but 80% seems pretty la=
rge.) &nbsp;Splitting and<o:p></o:p></p></blockquote><blockquote style=3D'm=
argin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal>various indexing =
artifacts can sometimes lead to this. &nbsp;I'd recommend<o:p></o:p></p></b=
lockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p cla=
ss=3DMsoNormal>running labelit.index on the images and seeing what it think=
s the<o:p></o:p></p></blockquote><blockquote style=3D'margin-top:5.0pt;marg=
in-bottom:5.0pt'><p class=3DMsoNormal>lattice should be.<o:p></o:p></p></bl=
ockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p clas=
s=3DMsoNormal><o:p>&nbsp;</o:p></p></blockquote><blockquote style=3D'margin=
-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal>-Nat<o:p></o:p></p></b=
lockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p cla=
ss=3DMsoNormal>_______________________________________________<o:p></o:p></=
p></blockquote><blockquote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><=
p class=3DMsoNormal>phenixbb mailing list<o:p></o:p></p></blockquote><block=
quote style=3D'margin-top:5.0pt;margin-bottom:5.0pt'><p class=3DMsoNormal><=
a href=3D"mailto:phenixbb at phenix-online.org">phenixbb at phenix-online.org</a>=
<o:p></o:p></p></blockquote><blockquote style=3D'margin-top:5.0pt;margin-bo=
ttom:5.0pt'><p class=3DMsoNormal><a href=3D"http://phenix-online.org/mailma=
n/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>=
<o:p></o:p></p></blockquote><p class=3DMsoNormal>__________________________=
_____________________<br>phenixbb mailing list<br><a href=3D"mailto:phenixb=
b at phenix-online.org">phenixbb at phenix-online.org</a><br><a href=3D"http://ph=
enix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman=
/listinfo/phenixbb</a><o:p></o:p></p></div></div><p class=3DMsoNormal><o:p>=
&nbsp;</o:p></p><div><p class=3DMsoNormal><span class=3Dapple-style-span><s=
pan style=3D'font-size:13.5pt;font-family:"Palatino","serif";color:black'>.=
.....................</span></span><span style=3D'font-size:13.5pt;font-fam=
ily:"Palatino","serif";color:black'><br><span class=3Dapple-style-span>J=FC=
rgen Bosch</span><br><span class=3Dapple-style-span>Johns Hopkins Universit=
y</span><br><span class=3Dapple-style-span>Bloomberg School of Public Healt=
h</span><br><span class=3Dapple-style-span>Department of Biochemistry &amp;=
 Molecular Biology</span><br><span class=3Dapple-style-span>Johns Hopkins M=
alaria Research Institute</span><br><span class=3Dapple-style-span>615 Nort=
h Wolfe Street, W8708</span><br><span class=3Dapple-style-span>Baltimore, M=
D 21205</span><br><span class=3Dapple-style-span>Office: +1-410-614-4742</s=
pan><br><span class=3Dapple-style-span>Lab: &nbsp; &nbsp; &nbsp;+1-410-614-=
4894</span><br><span class=3Dapple-style-span>Fax: &nbsp; &nbsp; &nbsp;+1-4=
10-955-2926</span><br><span class=3Dapple-style-span><a href=3D"http://web.=
mac.com/bosch_lab/">http://web.mac.com/bosch_lab/</a></span><br><br><br><br=
><br></span><o:p></o:p></p></div><p class=3DMsoNormal><o:p>&nbsp;</o:p></p>=
</div></div></body></html>=

--_000_D094A6D6EE131943B1CFB555758191F91229929C31NIHMLBXBB02ni_--

--_004_D094A6D6EE131943B1CFB555758191F91229929C31NIHMLBXBB02ni_
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