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Hi Carsten,<br>
<br>
<blockquote
cite="mid:204D6E1BD9ACEA40B3F76FE9C125528F044023E7@JNJUSSHGMS01.na.jnj.com"
type="cite">
<p dir="ltr"><span lang="en-us"><font face="Calibri">I was wondering
if anyone had experience/advice for real space refinement with phenix
using marginal data to 3A.</font></span><span lang="en-us"> <font
face="Calibri">I just did a run (SA, real-space refinement</font></span><span
lang="en-us"><font face="Calibri"> against diff_map</font></span><span
lang="en-us"><font face="Calibri">, 2 fold NCS, grouped APD</font></span><span
lang="en-us"><font face="Calibri">, fix_rotamers enabled</font></span><span
lang="en-us"><font face="Calibri">)</font></span><span lang="en-us"> <font
face="Calibri">were the resulting structure showed lots of
disconnected sidechains and some broken main chains.</font></span><span
lang="en-us"> <font face="Calibri">I am just repeating the run w/o
real space refinement,</font></span><span lang="en-us"><font
face="Calibri"> may be the combination of SA and real space refinement
was a bit harsh,</font></span><span lang="en-us"> <font face="Calibri">
but am wondering what kind of parameters make most sense to tweak in
order to avoid</font></span><span lang="en-us"> <font face="Calibri">having
the mole</font></span><span lang="en-us"><font face="Calibri">cules
fall apart.</font></span></p>
</blockquote>
<br>
this could be a weight issue (weight between real-space target and
restraints). In general I didn't find it too beneficial doing
real-space refinement globally, although I've seen cases where it made
a good difference (but at higher than 3A resolution). You may try to
switch to "simple" target (to make it run much faster) and turn on the
weight optimization:<br>
<br>
real_space_refinement {<br>
mode = *simple diff_map<br>
target_weights = value *grid_search gradients_ratio<br>
rmsd_max_bonds = 0.05<br>
rmsd_max_angles = 5<br>
grid_search_scales = 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3<br>
}<br>
<br>
<br>
"fix_rotamers=true" (local real-space refinement for the residues that
really need it, as determined automatically) is much better option. I
thoroughly tested it up to 3A resolution and in all test cases it
worked just great. Try it and see what happens for your data.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
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