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<div class="moz-cite-prefix">Hi Maxime,<br>
<br>
this problem is now addressed in phenix.refine and other related
tools (such as phenix.pdbtools, phenix.model_vs_data,
phenix.geometry_minimization): next available nightly build should
have it. The correct distances are used based on
"scattering_table=neutron" flag in phenix.refine and
phenix.model_vs_data, and "use_neutron_distances=true" in
phenix.pdbtools and phenix.geometry_minimization.<br>
<br>
Please let me know should you have any questions and notice any
problems.<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<br>
On 11/6/12 9:45 AM, Maxime Cuypers wrote:<br>
</div>
<blockquote
cite="mid:CACT_3tEW2=_NxeNJuJ0OoAzbBh-Ki9G=5Y6KLqxbmw5Bgez_DQ@mail.gmail.com"
type="cite">Hi,<br>
<br>
i am refining a perdeuterated neutron structure and have noticed a
lot of positive density aside the D atoms on aliphatic and
aromatic side chains. just in the alignment of C-D bonds (C-D then
+), suggesting that phenix.refine constraints these bond lengths
too short in my case. i tried automatic weights for geometry
refinement and unrestrained specific C-D refinement but it is not
satisfactory.<br>
<br>
then i found the following funny distances (angströms) in the pdb
database neutron structures:<br>
<br>
3KYX:<br>
program: Phenix.refine<br>
D-prot<br>
Distances: <br>
C-D aromatics = 0.93-0.94<br>
C-D aliph. = 0.98<br>
<br>
1CQ2<br>
Program : xplor3.1<br>
D-protein (despite the atoms being labelled as H according to
abstract)<br>
Distances: <br>
C-D aromatics = 1.06-1.08<br>
C-D aliph. = 1.08<br>
<br>
4FC1<br>
H-protein<br>
Distances: <br>
program: Phenix.refine<br>
C-H aromatics = 0.93<br>
C-H aliph. = 0.97<br>
<br>
1VCX<br>
H-protein<br>
program: CNS<br>
Distances: <br>
C-H aromatics = 1.06-1.10<br>
C-H aliph. = 1.09<br>
<br>
those neutron C-D/C-H bond lengths in pdb seem pretty much
inconsistentto me.<br>
<br>
So it seems that phenix.refine uses C-D/ C-H bonds restrains that
are different to other programs to below 1.0 Ang. ( ca. 0.10 A
differences) <br>
how can i change the restraints to make it all longer bond lengths
for C-D only? with a .cif file?<br>
i saw that phenix uses the CCP4 monomer library but the one in : <br>
/usr/local/phenix-.../chem_data/mon_lib/list<br>
only seem to be applying modifications. <br>
<br>
any clue on how to specifically modify the restraints parameters
on C-D bonds would be very appreciated.<br>
<br>
Thanks,<br>
<br>
Maxime<br>
<br>
<br>
<br>
<br>
<br>
<br>
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