phenix.refine doesn't support custom dihedrals. Sorry. For this you need to work with CIF links.<div><br></div><div>Coot ignores our edits. I'm not sure how it deals with CIF links. I hope someone else can help.</div>
<div><br></div><div>Ralf<br><br><div class="gmail_quote">On Mon, May 14, 2012 at 8:05 PM, Vitali Stanevich <span dir="ltr"><<a href="mailto:stanevich@wisc.edu" target="_blank">stanevich@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi again,<br><br>Thanks to your advices, I was able create bonds of desired length for phenix.refine. But I have 2 more questions:<br>
<br>1) Perhaps naive, but how do I define dihedral angle? I tried:<br><br>dihedral {<br>
���� atom_selection_1 = name C18 and chain G and resname 1ZN and resseq 5<br>���� atom_selection_2 = name C20 and chain G and resname 1ZN and resseq 5<br>���� atom_selection_3 = name N4 and chain G and resname FGA and resseq 6<br>
���� atom_selection_4 = name C4 and chain G and resname FGA and resseq 6<br>���� dihedral_ideal = 180<br>���� sigma = 5<br>��� } <br>And it was ignored by phenix.refine. Or dihedral is somehow defined just through the angles?<br>
<br>2) After I try to apply "real_space_refine" in coot to the ligand molecule - bonds which I defined in "edits" file break and my polymer again becomes several monomers. Is that normal?<br><br>Thanks again,<br>
Vitali<div class="HOEnZb"><div class="h5"><br><br><div class="gmail_quote">On Sun, May 13, 2012 at 6:42 PM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This may solve your problems. I used<br>
<br>
phenix.ligand_linking 3dw8.pdb<br>
<br>
in a recent version. You should read the article, however, as it will<br>
allow you to troubleshoot and obtain proof of linkage.<br>
<br>
Cheers<br>
<br>
Nigel<br>
<div><div><br>
On Sun, May 13, 2012 at 10:39 AM, Ralf Grosse-Kunstleve<br>
<<a href="mailto:rwgrosse-kunstleve@lbl.gov" target="_blank">rwgrosse-kunstleve@lbl.gov</a>> wrote:<br>
> See this newsletter:<br>
><br>
> <a href="http://www.phenix-online.org/newsletter/CCN_2011_01.pdf" target="_blank">http://www.phenix-online.org/newsletter/CCN_2011_01.pdf</a><br>
><br>
> pages 3-5: FAQ<br>
> There are two methods to add links between atoms in Phenix. Which one should<br>
> I use?<br>
><br>
> Let us know if this doesn't fully answer your question.<br>
><br>
> Ralf<br>
><br>
><br>
> On Sat, May 12, 2012 at 6:58 PM, Vitali Stanevich <<a href="mailto:stanevich@wisc.edu" target="_blank">stanevich@wisc.edu</a>><br>
> wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> I am trying to refine protein structure with MCLR ligand - this is cyclic<br>
>> hepta-peptide which has some non-standard amino acids. Sequence is<br>
>> DAL-LEU-ACB-ARG-1ZN-FGA-DAM. It's exactly the same compound as chain G at<br>
>> 3dw8 PDB entry.<br>
>><br>
>> I could successfully import amino acids in coot through "get monomer"<br>
>> option, renumber and combine in one chain. Problem is that whenever I use<br>
>> phenix.refine it returns all residues nonbonded. Corresponding carboxyl and<br>
>> amino groups are in close proximity to make a bond. I tried to write LINKR<br>
>> record in .pdb - with no success:<br>
>> ...<br>
>> LINKR������������ 1ZN G�� 5�������������������� FGA G�� 6<br>
>> trans<br>
>> LINKR������������ FGA G�� 6�������������������� DAM G�� 7<br>
>> trans<br>
>> ...<br>
>><br>
>> Is there a way to create peptide bonds in this inhibitor chain? I'm using<br>
>> phenix Version: 1.7.3.<br>
>><br>
>> Thanks in advance,<br>
>> Vitali<br>
>><br>
>><br>
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><br>
><br>
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<br>
<br>
<br>
</div></div><span><font color="#888888">--<br>
Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a>� �� Email : NWMoriarty@LBL.gov<br>
Fax�� : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a>� � �� Web� : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><br>
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