[phenixbb] Changing an amino acid to an unusual amino acid

Kevin Jude kjude at stanford.edu
Tue Jun 2 20:15:04 PDT 2015


I just went through this with a blue FP.  Carsten is correct about how to
define the peptide bonds, but an easier way is to use JLigand.  The
tutorial at
http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link is
helpful.  You will have to define the i-1 and i+1 links in separate .cif
files if you use JLigand.

HTH
kmj

On Tue, Jun 2, 2015 at 4:40 PM, Schubert, Carsten [JRDUS] <
CSCHUBER at its.jnj.com> wrote:

>  Hi Nat,
>
>
>
> bonds in COOT do not mean much, as they do not translate into bonded
> interactions in the refinement programs. Phenix for instance tries to
> figure out the bonding by itself through some distance based heuristics.
> However in your case it looks as if the CRO residue may not be defined as a
> polymer, i.e. part of a protein chain in the monomer library you are using.
> In Windows the monomer library is located in
> C:\WinCoot\share\coot\lib\data\monomers. Look at the difference in the
> headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The
> aminoacids or modified aminoacids considered part of the peptide chain have
> all ‘peptide’ in the header, CRO does not. That is probably the reason why
> coot does not make any bonds. This would probably cause problems later on
> with Phenix as well. You could pull out the CRO.cif into your directory,
> modify it to make it a peptide and read it into coot and phenix during
> refinement. I would also run it through REEL to make sure the definitions
> are kosher.
>
>
>
> HTH
>
>
>
>                 Carsten
>
>
>
>
>
> *From:* Natalia Ketaren [mailto:nketaren at mail.rockefeller.edu
> <nketaren at mail.rockefeller.edu>]
> *Sent:* Tuesday, June 02, 2015 5:42 PM
> *To:* Schubert, Carsten [JRDUS]
> *Subject:* Re: Changing an amino acid to an unusual amino acid
>
>
>
> Hi Carsten,
>
>
>
> Th residue is a part of the correct chain. It just doesn’t make an bonds
> with the residues on either side of it. Is this common for unusual amino
> acids when adding to the main chain?
>
>
>
> Cheers,
>
>
>
> Nat
>
> _____________________________
>
> Natalia E. Ketaren, PhD
> Postdoctoral Associate
> Rout Laboratory
> Box 213
> The Rockefeller University
> 1230 York Avenue
> New York, NY 10065
>
> Tel: (212) 327-8136
> Fax: (212) 327-7193
> Natalia.Ketaren at rockefeller.edu
> website: http://lab.rockefeller.edu/rout/
> NCDIR: http://www.ncdir.org/
>
>
>
> On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] <
> CSCHUBER at its.jnj.com> wrote:
>
>
>
> Hi Natalia,
>
>
>
> if the missing/wrong chain IDs are really the problem you can change them
> in COOT under Calculate -> Change Chain IDs. The dialog is a bit tricky,
> since you probably have to use the correct residue range to change an
> individual residue into an existing chain. In your case I would write out
> the PDB file and use a text editor to change the chain ID and move the
> residue into its correct place in the file.
>
>
>
> HTH
>
>
>
>                 Carsten
>
>
>
> *From:* phenixbb-bounces at phenix-online.org [
> mailto:phenixbb-bounces at phenix-online.org
> <phenixbb-bounces at phenix-online.org>] *On Behalf Of *Natalia Ketaren
> *Sent:* Tuesday, June 02, 2015 5:17 PM
> *To:* phenixbb at phenix-online.org
> *Subject:* [phenixbb] Changing an amino acid to an unusual amino acid
>
>
>
> Hello All,
>
>
>
> I’m working on a GFP structure and I’m trying to incorporate the CRO
> (chromophore) residue into the structure using coot. My process is to use
> Extension->Modelling—>Replace residues, where it’s suppose to replace a Tyr
> residue. I type the 3 letter code, CRO, the residue appears, I’m able to
> real space refine it, but it does not incorporate CRO into the desired
> chain. Would someone be able to help me figure out what I’m doing wrong?
> And possibly walk me through a solution?
>
>
>
> Cheers,
>
>
>
> Nat
>
> _____________________________
>
> Natalia E. Ketaren, PhD
> Postdoctoral Associate
> Rout Laboratory
> Box 213
> The Rockefeller University
> 1230 York Avenue
> New York, NY 10065
>
> Tel: (212) 327-8136
> Fax: (212) 327-7193
> Natalia.Ketaren at rockefeller.edu
> website: http://lab.rockefeller.edu/rout/
> NCDIR: http://www.ncdir.org/
>
>
>
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