[phenixbb] Sugar woes

[Nigel Moriarty]

Simon

Things have improved since last December's version 1.7.3 but rather
than install a nightly build I believe you can solve your problems by
using the attached files. One program that can help a lot is CarboLoad
which will load a carbohydrate into your model without having to
fiddle with Coot. I would install a nightly build, however, if you
wish to get some great new features.

Cheers

Nigel

PS.

  CarboLoad - A program for loading carbohydrates into a protein model


Usage:
  phenix.carbo_load protein_pdb_file_name=pdb3a37.ent \
                    carbohydrate_file_name=man.txt \
                    map_coeffs_file_name=pdb3a36_map_coeffs.mtz \
                    residue_selection="resname LG1"


You can even specify the carbohydrate using the string "NAG-NAG-MAN".
Contact me for any help you require.

On Tue, Apr 17, 2012 at 3:18 AM, Simon Kolstoe <s.kolstoe at ucl.ac.uk> wrote:
> Hi phenixbb,
>
> Every couple of years I come to build a sugar chain into a protein structure and hope the process is less painful than last time, however it seems things still are not smooth yet!
>
> I'm trying to build a fairly standard sugar chain onto a protein and am encountering many problems. What I am doing is using coot to get the coordinates for each sugar using the "File-> Get monomer" option and then putting the appropriate link in my phenix.refine .def file after renumbering the sugars. For example:
>
> apply_cif_link {
>      data_link = "BETA1-2"
>      residue_selection_1 = chain Z and resname NAG and resid 5
>      residue_selection_2 = chain Z and resname MAN and resid 4
>    }
>    apply_cif_link {
>      data_link = "BETA1-4"
>      residue_selection_1 = chain Z and resname GAL and resid 6
>      residue_selection_2 = chain Z and resname NAG and resid 5
>    }
>
>  For some reason I keep getting the following error:
>
> ---------------
>
> Chain: "Z"
>      Number of atoms: 220
>      Number of conformers: 1
>      Conformer: ""
> Sorry: Traceback (most recent call last):
>  File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1042, in apply_mod
>    mod_mon = self.monomer.apply_mod(mod_mod_id)
>  File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 399, in apply_mod
>    result.delete_atom_in_place(mod_atom.atom_id)
>  File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/monomer_library/cif_types.py", line 316, in delete_atom_in_place
>    raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id)
> RuntimeError: delete_atom_in_place: unknown atom_id: HO2
> apply_mod failure:
>  pdbres="NAG Z   5 " segid="Z   "
>  comp id: NAG-b-D
>  mod id: DEL-HO2
>
> ------------------
>
> I haven't deleted the hydrogens that came with the sugars so what I thought it was doing was trying to delete an atom that isn't there, however adding a dummy atom with the name HO2 didn't work - any ideas?
>
> Also it seems happy with BETA1-4 links but not ALPHA2-6 links? How do I specify this link?
>
> Thanks,
>
> Simon
>
>
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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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