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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi
Gino, Tom and Randy, <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I
would rather argue for a future “specialized” phenix low res molecular
replacement application/wizard than for simple conversion to throw an EM
map into a standard MR procedure. In my experience, MR with EM models is
significantly more complex than with a molecular model for several reasons. For
example, <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>the
EM maps may suffer from scaling errors which can have a severe impact on
packing function scores and downstream averaging procedures, so an
automatic “scale grid search” would be really useful. <o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>EM
maps sometimes are affected by accumulation of density along axes of symmetry
of particles which can severely bias the outcome. Sometimes grid searches
for the origin of symmetry combined with initial low-res averaging steps are
helpful. <o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Maps
without an associated molecular model are difficult to break into conformationally
rigid parts. Although many EM structures are derived on the basis of
conformational classification or sorting, this information is not usually
presented in a useful way in publications or database depositions. <o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Negative
stain (cryo) EM maps are particular prone to conformation distortions due to
staining artifacts.<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>For
particles with strongly preferred orientations on the EM grid, the maps may
have some special features <o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>…<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>A
preferred application for (low-res) MR from EM maps ( or also SAXS data ???)
would ideally be able to solve some of these problems. A plain density to
structure factor conversion as an entry to standard MR can already easily be
done manually. But if it’s done automatically without overcoming the
above problems, many research will once try “automated MR from EM” through
wizard X. If this ends unsuccessfully, they may believe their problem could
simply not be solved and feel discouraged from investing a little more time and
finally miss a chance to solve their problems. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Cheers,
<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
Timm<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Dr.
Timm Maier<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>ETH
Zurich<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Institute
of Molecular Biology and Biophysics<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>HPK
H 5 <o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Schafmattstr.
20<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>8093
Zurich<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>SWITZERLAND<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE-CH style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>e-mail:
timm.maier@mol.biol.ethz.ch<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>phone
++41 44 633 3148<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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