<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Yes, I am aware of the disadvantage that the ramachandran plot is no longer a validation tool if the phi-psi angels are restrained. However, in the situation of low-resolution structure, the electron density is not really good enough to confine the backbones. Since the backbones can move around in the electron density without making differences in the refinement, why not restrain the phi-psi angels to those we know are correct. Shouldn't them be better than the conformations with phi-psi angles that we know are not correct? If the refinement program can't give me a better ramachandran plot, I probably will manually correct them in a modeling program like coot, which is tedious. I heard Paul Emsley has a plan to build ramachandran plot target into the real space refinement in Coot. It is not available in Coot last time I checked.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Adding riding hydrogens into the structure was a powerful validation tool. But now we all add riding hydrogens into the refinement since it makes the refinement better. At the same time, we lose some power in the validation. We still think it is worth doing so, don't we?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Jianghai</DIV><DIV><BR class="khtml-block-placeholder"><DIV><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>+++++++++++++++++++++++++++++++</DIV><DIV>Jianghai Zhu, Ph.D</DIV><DIV>CBR Institute for Biomedical Research</DIV><DIV>Department of Pathology</DIV><DIV>Harvard Medical School</DIV><DIV>200 Longwood Ave., Boston, MA 02115</DIV><DIV>Ph: 617-278-3211</DIV><DIV>Fx: 618-278-3232</DIV><DIV>+++++++++++++++++++++++++++++++</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN> </DIV><BR><DIV><DIV>On Jul 25, 2007, at 10:57 PM, Pavel Afonine wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> 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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