[phenixbb] Restraints file for a new amino acid residue

Wed Nov 14 13:15:48 PST 2012

It would be better to fix the model. The edits you mention also have a
cutoff of 3 angstrom by default so you'd have to change it.

You can increase the automatic cutoff distance using the phil parameter
peptide_nucleotide_distance_cutoff but it's always better to have a model
with residues within 3 angstroms.

Nigel

On Wed, Nov 14, 2012 at 12:25 PM, Kip Guja <kip at pharm.stonybrook.edu> wrote:

> Hi Nigel,
>
> Thank you for the clarification, I appreciate it!
>
> So in this specific case maybe one possible solution is to use geometry
> restraints to bring the atoms close enough to form the bond in question?
>
> Something like this was previously described by Pavel here:
> http://www.phenix-online.org/**pipermail/phenixbb/2008-**
> January/011977.html<http://www.phenix-online.org/pipermail/phenixbb/2008-January/011977.html>
>
> Kip
>
>
>
>
>
>
>
>
>
> On Wed, 14 Nov 2012 12:10:23 -0800
>  Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>
>> 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-**<http://www.phenix-online.org/**pipermail/phenixbb/2008-**>
>>> January/011981.html<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-**<http://www.phenix-online.org/**pipermail/phenixbb/2010-**>
>>>>> August/015629.html<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>
>>>>> <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
>>>>
>>>>
>>> ______________________________****_________________
>>> phenixbb mailing list
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>>> <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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