[phenixbb] Restraints file for a new amino acid residue

[Nigel Moriarty]

Kip

PHENIX doesn't use the "L-peptide" field in the automatic linking of amino
acids. It's based on

1. the sequence in the model
2. the bond distance cutoff (3.0 from memory)
3. the atom names in the residue (C, N, CA, O)

Cheers

Nigel

On Wed, Nov 14, 2012 at 11:55 AM, Kip Guja <kip at pharm.stonybrook.edu> wrote:

> It may be a good idea to open your cif file in a text
> editor and check that the residue type is specified correctly
> -- 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" that
> you observe.
>
> This previous discussion may also be helpful:
> http://www.phenix-online.org/**pipermail/phenixbb/2008-**
> January/011981.html<http://www.phenix-online.org/pipermail/phenixbb/2008-January/011981.html>
>
> Example Alanine cif file:
> #
> data_comp_list
> loop_
> _chem_comp.id
> _chem_comp.three_letter_code
> _chem_comp.name
> _chem_comp.group
> _chem_comp.number_atoms_all
> _chem_comp.number_atoms_nh
> _chem_comp.desc_level
> _chem_comp.initial_date
> _chem_comp.modified_date
> _chem_comp.source
> 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 confidence.
>>
>>
>> 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 (covalently)
>>>  modified residue. The colosest discussion to our problem is:
>>>
>>>
>>> http://www.phenix-online.org/**pipermail/phenixbb/2010-**
>>> August/015629.html<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<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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>



-- 
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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