Send me the PDB file and I'll work on getting the correct links for you. You can send just the two residues involved off-list if you like.<div><br></div><div>Nigel</div><div><br></div><div>NB. Any files sent to me will be held in strictest confidence.<br>
<br><br><div class="gmail_quote">On Wed, Apr 3, 2013 at 8:11 PM, David Shin <span dir="ltr"><<a href="mailto:davidsshin@lbl.gov" target="_blank">davidsshin@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi -<div><br></div><div>I was trying to resolve some issues where I have an acetyl group at the N-terminus. Historically it appears, these are treated as a residue (say "ACE 0"). To provide phenix.refine with angles and bonds, I made a file similar to a metal.edits file:</div>
<div><br></div><div>One example of an angle between the acetyl and the first amino acid in my file:</div><div><div>refinement.geometry_restraints.edits {</div><div>� angle {</div><div>� � action = *add</div><div>� � atom_selection_1 = name C � and chain A and resname ACE and resseq � 0</div>
<div>� � atom_selection_2 = name N � and chain A and resname ALA and resseq � 1</div><div>� � atom_selection_3 = name CA �and chain A and resname ALA and resseq � 1</div><div>� � angle_ideal = 121.6367</div><div>� � sigma = 5</div>
<div>� }</div><div>}</div><div><br></div><div>The problem I'm having is defining a plane such that what would appear to be a peptide bond is flat: ACE O - ACE C - ALA N - ALA H</div><div>I'm just not sure if it's being taken care of, there is a slight bend after refinement, but this also matches the electron density somewhat.</div>
<div><br></div><div>I tried to run elbow.ligand_linking , but appears to be missing from the release I have: �phenix-1.8.2-1309</div><div><br></div><div>Anything help appreciated.</div><div><br></div><div>Thanks,</div><div>
<br></div><div>Dave</div><div><div class="h5"><br><div class="gmail_quote">On Mon, Jan 30, 2012 at 12:36 AM, Christian Roth <span dir="ltr"><<a href="mailto:christian.roth@bbz.uni-leipzig.de" target="_blank">christian.roth@bbz.uni-leipzig.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
thanks to the phenix team which helped me a lot to resolve all issues<br>
regarding the correct link definitions.<br>
<br>
I have summarised a few things which one might consider if nonstandard links<br>
are necessary.<br>
<br>
Try phenix ready set to get your links out of the pdb. Do not forget to change<br>
the possible LINKR to LINK!<br>
Inspect the links and decide if they are useful!<br>
Peptide links are automatically incorporated if residues are close (inspect<br>
geo file)<br>
Non standard peptide links could be created using using an now available alpha<br>
release script:<br>
<br>
elbow.ligand_linking model.pdb<br>
<br>
Inspect the generated cif file and correct angles and incorporate dihedrals and<br>
so on if necessary.<br>
<br>
Sugar links which exists in the mon_lib.cif should be incorporated using the<br>
apply_cif link option like<br>
refinement.pdb_interpretation.apply_cif_link {<br>
� � �data_link = ALPHA1-4<br>
� � �residue_selection_1 = chain B and resname GLC and resseq � �1<br>
� � �residue_selection_2 = chain B and resname GLC and resseq � �2<br>
}<br>
According to the link definition the C1 oxygen of the following sugar with the<br>
higher number must be removed.<br>
The automatic incorporation of sugar links will be probably soon available in<br>
phenix. Nigel is already working on this.<br>
If one want use hydrogens in the refinement, they have to be added previously<br>
with ready_set and afterwards the OH4 sugar hydrogen has to be removed before<br>
the refinement.<br>
<br>
For links with symmetry related atoms the symmetry operator must be included<br>
in a custom bond definition<br>
efinement.geometry_restraints.edits {<br>
� bond {<br>
� � action = *add delete change<br>
� � atom_selection_1 = chain A and resname HEM and resid 154 and name FE<br>
� � atom_selection_2 = chain A and resname MTO and resid 155 and name O<br>
� � symmetry_operation = -x,y,-z<br>
� � distance_ideal = 2.2<br>
� � sigma = 0.01<br>
� }<br>
}<br>
The operator can be obtained using<br>
<br>
iotbx.show_distances your.pdb > all_distances<br>
<br>
Search for keyword "sym"<br>
or from Coot clicking on the symm option. Coot print out the operator and the<br>
translation term separately. Both has to be merged in the �final operator used<br>
in phenix!<br>
<br>
Christian<br>
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</blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br><div>David Shin, Ph.D</div><div>Lawrence Berkeley National Labs</div><div>1 Cyclotron Road</div><div>MS 83-R0101</div>
<div>Berkeley, CA 94720</div><div>USA</div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709� �� Email : NWMoriarty@LBL.gov<br>
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