[phenixbb] links in phenix summary

Nigel Moriarty nwmoriarty at lbl.gov
Wed Apr 3 21:06:50 PDT 2013


Send me the PDB file and I'll work on getting the correct links for you.
You can send just the two residues involved off-list if you like.

Nigel

NB. Any files sent to me will be held in strictest confidence.


On Wed, Apr 3, 2013 at 8:11 PM, David Shin <davidsshin at lbl.gov> wrote:

> Hi -
>
> I was trying to resolve some issues where I have an acetyl group at the
> N-terminus. Historically it appears, these are treated as a residue (say
> "ACE 0"). To provide phenix.refine with angles and bonds, I made a file
> similar to a metal.edits file:
>
> One example of an angle between the acetyl and the first amino acid in my
> file:
> refinement.geometry_restraints.edits {
>   angle {
>     action = *add
>     atom_selection_1 = name C   and chain A and resname ACE and resseq   0
>     atom_selection_2 = name N   and chain A and resname ALA and resseq   1
>     atom_selection_3 = name CA  and chain A and resname ALA and resseq   1
>     angle_ideal = 121.6367
>     sigma = 5
>   }
> }
>
> The problem I'm having is defining a plane such that what would appear to
> be a peptide bond is flat: ACE O - ACE C - ALA N - ALA H
> I'm just not sure if it's being taken care of, there is a slight bend
> after refinement, but this also matches the electron density somewhat.
>
> I tried to run elbow.ligand_linking , but appears to be missing from the
> release I have:  phenix-1.8.2-1309
>
> Anything help appreciated.
>
> Thanks,
>
> Dave
>
> On Mon, Jan 30, 2012 at 12:36 AM, Christian Roth <
> christian.roth at bbz.uni-leipzig.de> wrote:
>
>> Dear all,
>>
>> thanks to the phenix team which helped me a lot to resolve all issues
>> regarding the correct link definitions.
>>
>> I have summarised a few things which one might consider if nonstandard
>> links
>> are necessary.
>>
>> Try phenix ready set to get your links out of the pdb. Do not forget to
>> change
>> the possible LINKR to LINK!
>> Inspect the links and decide if they are useful!
>> Peptide links are automatically incorporated if residues are close
>> (inspect
>> geo file)
>> Non standard peptide links could be created using using an now available
>> alpha
>> release script:
>>
>> elbow.ligand_linking model.pdb
>>
>> Inspect the generated cif file and correct angles and incorporate
>> dihedrals and
>> so on if necessary.
>>
>> Sugar links which exists in the mon_lib.cif should be incorporated using
>> the
>> apply_cif link option like
>> refinement.pdb_interpretation.apply_cif_link {
>>      data_link = ALPHA1-4
>>      residue_selection_1 = chain B and resname GLC and resseq    1
>>      residue_selection_2 = chain B and resname GLC and resseq    2
>> }
>> According to the link definition the C1 oxygen of the following sugar
>> with the
>> higher number must be removed.
>> The automatic incorporation of sugar links will be probably soon
>> available in
>> phenix. Nigel is already working on this.
>> If one want use hydrogens in the refinement, they have to be added
>> previously
>> with ready_set and afterwards the OH4 sugar hydrogen has to be removed
>> before
>> the refinement.
>>
>> For links with symmetry related atoms the symmetry operator must be
>> included
>> in a custom bond definition
>> efinement.geometry_restraints.edits {
>>   bond {
>>     action = *add delete change
>>     atom_selection_1 = chain A and resname HEM and resid 154 and name FE
>>     atom_selection_2 = chain A and resname MTO and resid 155 and name O
>>     symmetry_operation = -x,y,-z
>>     distance_ideal = 2.2
>>     sigma = 0.01
>>   }
>> }
>> The operator can be obtained using
>>
>> iotbx.show_distances your.pdb > all_distances
>>
>> Search for keyword "sym"
>> or from Coot clicking on the symm option. Coot print out the operator and
>> the
>> translation term separately. Both has to be merged in the  final operator
>> used
>> in phenix!
>>
>> Christian
>> _______________________________________________
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>
>
>
> --
> David Shin, Ph.D
> Lawrence Berkeley National Labs
> 1 Cyclotron Road
> MS 83-R0101
> Berkeley, CA 94720
> USA
>
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> 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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