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] < [email protected]> 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:[email protected] ] *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 [email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] < [email protected]> 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:* [email protected] [ mailto:[email protected] ] *On Behalf Of *Natalia Ketaren *Sent:* Tuesday, June 02, 2015 5:17 PM *To:* [email protected] *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 [email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

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On 03/06/15 00:40, Schubert, Carsten [JRDUS] wrote:

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.

I think that you're right.

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.

That's right.

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.

Edit -> Restaints -> CRO -> [Group] -> {modify to} L-peptide [Return] -> Apply Paul.