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

Nigel Moriarty nwmoriarty at lbl.gov
Wed Jun 3 10:16:10 PDT 2015


Natalia

I have attached a restraints file that should automatically link. I
generated the file with eLBOW and then edited that atom names to be the
standard main chain names. If you edit the PDB file to reflect the atoms it
should use the standard peptide links.

For the record, I changed

N1 -> N
CA1 -> CA
C3 -> C
O3 -> O

Cheers

Nigel

---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Jun 2, 2015 at 8:15 PM, Kevin Jude <kjude at stanford.edu> wrote:

> 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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>
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