<div dir="ltr">Hi Zhijie,<div><br></div><div>Thank you very much for the information. For step 1 you mentioned, I can get monomer with L-Asp but it seems I can not drag it (or I do not know how to do) and can not delete or modify it to become isoAsp. I will try play around more though.</div><div><br></div><div>Xiao</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 17, 2015 at 6:33 PM, Zhijie Li <span dir="ltr"><<a href="mailto:zhijie.li@utoronto.ca" target="_blank">zhijie.li@utoronto.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
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<div>Hi Xiao,</div>
<div> </div>
<div>IsoAsp is essentially an L-Asp linked with next aa through its side chain
(beta) carboxyl. So the mutation button won’t help you. You need to build in a
new L-ASP, which is treated as a covalently linked ligand (HETATM records),
instead of a standard residue (ATOM records) of the protein chain.</div>
<div> </div>
<div>A practical method might be: 1) delete the original Asp, 2) import a free
L-Asp using “get monomer”, delete its hydrogen atoms and drag it into the
density, delete one oxygen atom on the beta-carboxyl and change the residue’s
numbering and chain id to fit it into the sequence, 3) edit the PDB, if
necessary, to turn the ASP into a ligand (a HETATM record inside the
chain).</div>
<div> </div>
<div>For step 3, you may need to rename the ASP to something else (IAS was used
for isoASP in older pdb, so I would go with IAS ) so that coot won’t try to make
a regular peptide bond using its main chain carboxyl during real space
refinement. Of course you will need to make a cif file for the “new” compound
too. I guess you can make a copy of ASP.cif from the monomer library and change
everything in it to IAS. I think if you have placed the IAS to the right
location and its ends are in bonding distance with the neighbouring aa residues
you may not need to do anything for refmac. For phenix.refine you will need to
add a bond description to the .edit file for each linkage the IAS makes to the
neighboring aas.</div>
<div> </div>
<div>You may take a look at the structure 1AT6 and its PDB file. The residue IAS
101 is an example of isoASP. Note that the IAS atoms are HETATM in the chain and
there are two LINK records in the header to indicate its linkage to neighbouring
aas (LINK records are normally not generated or needed during refinement using
refmac or phenix.refine). </div>
<div> </div>
<div> </div>
<div>Zhijie</div>
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<div style="BACKGROUND:#f5f5f5">
<div><b>From:</b> <a title="xiaoleiusc@gmail.com" href="mailto:xiaoleiusc@gmail.com" target="_blank">Xiao Lei</a> </div>
<div><b>Sent:</b> Monday, August 17, 2015 6:50 PM</div>
<div><b>To:</b> <a title="phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org" target="_blank">PHENIX user mailing list</a> </div>
<div><b>Subject:</b> [phenixbb] Coot mutation of Asp residue to isoAsp
residue</div></div></div>
<div> </div></div>
<div style="FONT-STYLE:normal;DISPLAY:inline;FONT-FAMILY:'Calibri';COLOR:#000000;FONT-SIZE:small;FONT-WEIGHT:normal;TEXT-DECORATION:none"><div><div class="h5">
<div dir="ltr">Dear Phenixbb members,
<div> </div>
<div>I suspect one Asp residue in my model may be an isoAsp (isomerization of
Asp). I am asking if there is way to mutate Asp residue to isoAsp(isoaspartic
acid) residue in coot GUI (I'm using coot 0.8.1 EL in Mac OS X10.10.5)?</div>
<div> </div>
<div>I know there is a mutation button on coot, but the mutated aa lists are all
natural amino acids. If I have to delete the Asp residue first and then build
isoAsp into the density map, is there a way in coot to build an isoAsp residue
in map?</div>
<div> </div>
<div>Thanks ahead.</div>
<div> </div>
<div>Xiao</div></div>
</div></div><p>
</p><hr>
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