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

Schubert, Carsten [JRDUS] CSCHUBER at its.jnj.com
Tue Jun 2 14:26:26 PDT 2015

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.



From: phenixbb-bounces at phenix-online.org [mailto: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?


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<mailto:Natalia.Ketaren at rockefeller.edu>
website: http://lab.rockefeller.edu/rout/
NCDIR: http://www.ncdir.org/

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