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Hi,<br>
<br>
you may want to read this before (yes, I remember, you deal with low
resolution structure and the information from this link may not be 100%
relevant to your case, but it is good to have a look anyway):<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html">http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html</a><br>
<br>
Cheers,<br>
Pavel.<br>
<br>
<br>
<br>
Ralf W. Grosse-Kunstleve wrote:
<blockquote cite="mid200707260057.l6Q0v8MG010357@cci.lbl.gov"
type="cite">
<pre wrap="">Hi Jianghai,
</pre>
<blockquote type="cite">
<pre wrap="">I am refining a low resolution huge protein structure. There are
about 20% residues in the disallowed region of ramachandran plot. Is
there a way in phenix.refine to refine the phi, psi angles to get a
better ramachandran plot? or a phi, psi restraints in refinement?
</pre>
</blockquote>
<pre wrap=""><!---->
If you add
discard_psi_phi=False
to the phenix.refine command line the psi and phi dihedral angles
are restraint according to the CCP4 monomer library definitions
in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get
the full path name). Look for data_link_TRANS and data_link_CIS,
scroll down to _chem_link_tor.value_angle, to see the restraint
definitions.
We don't have much experience using the phi, psi restraints.
If you don't mind, please let us know how it goes!
Ralf
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</pre>
</blockquote>
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