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<DIV>Hi Xiao,</DIV>
<DIV> </DIV>
<DIV>The previous IAS.cif I sent had the OXT atom missing. Please find the
attached IAS_mon_lib.cif, which has this mistake fixed.</DIV>
<DIV> </DIV>
<DIV>Zhijie</DIV>
<DIV> </DIV>
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<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><B>From:</B> <A title=xiaoleiusc@gmail.com
href="mailto:xiaoleiusc@gmail.com">Xiao Lei</A> </DIV>
<DIV><B>Sent:</B> Tuesday, August 18, 2015 1:56 PM</DIV>
<DIV><B>To:</B> <A title=zhijie.li@utoronto.ca
href="mailto:zhijie.li@utoronto.ca">Zhijie Li</A> </DIV>
<DIV><B>Cc:</B> <A title=phenixbb@phenix-online.org
href="mailto:phenixbb@phenix-online.org">PHENIX user mailing list</A> </DIV>
<DIV><B>Subject:</B> Re: [phenixbb] Coot mutation of Asp residue to isoAsp
residue</DIV></DIV></DIV>
<DIV> </DIV></DIV>
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<DIV dir=ltr>Hi Zhejie,
<DIV> </DIV>
<DIV>For the 1AT6 structure, I downloaded its density in coot using "fetch
density from EDS", but when I found the IAS at 101 position and try to do real
space refine, it gives an error that "Refinement setup failure. Failed to find
restraints for IAS." </DIV>
<DIV> </DIV>
<DIV>I do not know how to fix this but it seems to me it's caused by incomplete
restraints dictionary or monomer library in ccp4?</DIV>
<DIV> </DIV>
<DIV>Thanks.</DIV>
<DIV> </DIV>
<DIV>Xiao</DIV></DIV>
<DIV class=gmail_extra>
<DIV> </DIV>
<DIV class=gmail_quote>On Tue, Aug 18, 2015 at 10:42 AM, Xiao Lei <SPAN
dir=ltr><<A href="mailto:xiaoleiusc@gmail.com"
target=_blank>xiaoleiusc@gmail.com</A>></SPAN> wrote:<BR>
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<DIV dir=ltr>Hi Zhijie,
<DIV> </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><SPAN class=HOEnZb><FONT color=#888888>
<DIV> </DIV>
<DIV>Xiao</DIV></FONT></SPAN></DIV>
<DIV class=HOEnZb>
<DIV class=h5>
<DIV class=gmail_extra>
<DIV> </DIV>
<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>
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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><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<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>
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<DIV>
<DIV>
<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>
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