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@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
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@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@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
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
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Building 64R0246B, Physical Biosciences Division
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Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web :
CCI.LBL.gov