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@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@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@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@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@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] On Behalf Of Natalia Ketaren
Sent: Tuesday, June 02, 2015 5:17 PM
To: phenixbb@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@rockefeller.edu
website: http://lab.rockefeller.edu/rout/
NCDIR: http://www.ncdir.org/

 


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