[phenixbb] Restraints file for a new amino acid residue

Kip Guja kip at pharm.stonybrook.edu
Wed Nov 14 11:55:36 PST 2012

It may be a good idea to open your cif file in a text
editor and check that the residue type is specified 
-- in this case, it should be "L-peptide"

Here's a few lines for the alanine cif file as an example.
Note where it says "L-peptide" -- I could be wrong but I
believe this enables phenix to recognize that it should be
linked (form bonds) with adjacent amino acid residues.
Sometimes Elbow will create a cif file that says "Ligand"
in this field, which may be related to the "missing bond" 
you observe.

This previous discussion may also be helpful:

Example Alanine cif file:
ALA   ALA 'Alanine' L-peptide    10   5 .

On Wed, 14 Nov 2012 10:13:58 -0800
  Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
> Agnes
> It should link automatically if the criteria as listed in 
>the previous post
> are followed. You can check it in the .geo file. I'm 
>happy to take a look
> at it if you send me the model or even just the three 
>residues involved on
> list.
> Nigel
> NB. Any files sent to me will be held in strictest 
> On Wed, Nov 14, 2012 at 10:07 AM, Agnes Thiane Pereira 
>Machado <
> agnes_thiane at hotmail.com> wrote:
>> Hi
>>  We are trying to refine a protein structure with a 
>>  modified residue. The colosest discussion to our problem 
>> http://www.phenix-online.org/pipermail/phenixbb/2010-August/015629.html
>>  We ran:
>> phenix.elbow --residue SSC ourmodel.pdb
>>    And read the due cif file at phenix refinement. The 
>>residue by itself is OK, but we were
>>  not able to perform the peptide bond between C and N.
>> How to complete the .cif file such that it has due 
>>restraints for
>>  the peptide bond with this modified residue?
>>  Agnes
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> -- 
> 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

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