[phenixbb] NAG-NAG link definition seems to have no effect
Benjamin Stauch
bs448c at gmail.com
Thu Jun 12 01:55:53 PDT 2014
Thanks for your quick reply! However now I get the following error message,
"Fatal problems interpreting model file: NUmber of atoms with unkown
nonbonded energy type symbols: 3 Please edit the model file to resolve the
problems nd/org supply a CIF file with matching restraint definitions,
along with apply_cif_modification and apply_cif_link parameter definitions
if necessary. Alternatively, to continue despite this problem use:
stop_for_unknown=False"
the log file says,
Monomer Library directory:
"c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib"
Total number of atoms: 11298
Number of models: 1
apply_cif_link:
data_link: NAG-ASN
mod_id_1: DEL-O1
mod_id_2: DEL-HD22
residue_selection_1: chain A and resname NAG and resid 401
residue_selection_2: chain A and resname ASN and resid 74
apply_cif_link:
data_link: BETA1-4
mod_id_1: DEL-HO4
mod_id_2: DEL-O1
residue_selection_1: chain A and resname NAG and resid 401
residue_selection_2: chain A and resname NAG and resid 402
apply_cif_link:
data_link: NAG-ASN
mod_id_1: DEL-O1
mod_id_2: DEL-HD22
residue_selection_1: chain B and resname NAG and resid 401
residue_selection_2: chain B and resname ASN and resid 74
apply_cif_link:
data_link: BETA1-4
mod_id_1: DEL-HO4
mod_id_2: DEL-O1
residue_selection_1: chain B and resname NAG and resid 401
residue_selection_2: chain B and resname NAG and resid 402
Model: ""
Number of chains: 4
Chain: "A"
Number of atoms: 5075
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 319, 4675
Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}
Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}
Classifications: {'undetermined': 2, 'peptide': 317}
Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1,
'NH3': 1}
Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2}
Not linked:
pdbres="ALA A 317 " segid="A "
pdbres="NAG A 401 " segid="A "
Not linked:
pdbres="NAG A 401 " segid="A "
pdbres="NAG A 402 " segid="A "
Conformer: "B"
Number of residues, atoms: 319, 4675
Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}
Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}
Classifications: {'undetermined': 2, 'peptide': 317}
Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1,
'NH3': 1}
Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2}
Not linked:
pdbres="ALA A 317 " segid="A "
pdbres="NAG A 401 " segid="A "
Not linked:
pdbres="NAG A 401 " segid="A "
pdbres="NAG A 402 " segid="A "
bond proxies already assigned to first conformer: 4309
Chain: "B"
[...]
Chain: "C"
[...]
Residues with excluded nonbonded symmetry interactions: 26
residue:
[...]
Number of atoms with unknown nonbonded energy type symbols: 3
"ATOM 5046 HO4 NAG A 401 .*.A H "
"ATOM 6215 HD22 ASN B 74 .*.B H "
"ATOM 10057 HO4 NAG B 401 .*.B H "
Time building chain proxies: 4.05, per 1000 atoms: 0.36
Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do the
trick - as I explicitly want to refine hydrogens I reckon they are added
back on. Also it seems BETA1-4 wants to desperately link NAG O4 to NAG O1
which doesn't exist .. Shuld I manually define my NAG-NAG link instead of
using the BETA1-4?
Thanks again!
B
2014-06-12 10:54 GMT+02:00 Benjamin Stauch <bs448c at gmail.com>:
> Thanks for your quick reply! However now I get the following error message,
>
> "Fatal problems interpreting model file: NUmber of atoms with unkown
> nonbonded energy type symbols: 3 Please edit the model file to resolve the
> problems nd/org supply a CIF file with matching restraint definitions,
> along with apply_cif_modification and apply_cif_link parameter definitions
> if necessary. Alternatively, to continue despite this problem use:
> stop_for_unknown=False"
>
> the log file says,
>
>
>
> Monomer Library directory:
> "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib"
> Total number of atoms: 11298
> Number of models: 1
> apply_cif_link:
> data_link: NAG-ASN
> mod_id_1: DEL-O1
> mod_id_2: DEL-HD22
> residue_selection_1: chain A and resname NAG and resid 401
> residue_selection_2: chain A and resname ASN and resid 74
> apply_cif_link:
> data_link: BETA1-4
> mod_id_1: DEL-HO4
> mod_id_2: DEL-O1
> residue_selection_1: chain A and resname NAG and resid 401
> residue_selection_2: chain A and resname NAG and resid 402
> apply_cif_link:
> data_link: NAG-ASN
> mod_id_1: DEL-O1
> mod_id_2: DEL-HD22
> residue_selection_1: chain B and resname NAG and resid 401
> residue_selection_2: chain B and resname ASN and resid 74
> apply_cif_link:
> data_link: BETA1-4
> mod_id_1: DEL-HO4
> mod_id_2: DEL-O1
> residue_selection_1: chain B and resname NAG and resid 401
> residue_selection_2: chain B and resname NAG and resid 402
> Model: ""
> Number of chains: 4
> Chain: "A"
> Number of atoms: 5075
> Number of conformers: 2
> Conformer: "A"
> Number of residues, atoms: 319, 4675
> Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}
> Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}
> Classifications: {'undetermined': 2, 'peptide': 317}
> Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1,
> 'NH3': 1}
> Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2}
> Not linked:
> pdbres="ALA A 317 " segid="A "
> pdbres="NAG A 401 " segid="A "
> Not linked:
> pdbres="NAG A 401 " segid="A "
> pdbres="NAG A 402 " segid="A "
> Conformer: "B"
> Number of residues, atoms: 319, 4675
> Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1}
> Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1}
> Classifications: {'undetermined': 2, 'peptide': 317}
> Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1,
> 'NH3': 1}
> Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2}
> Not linked:
> pdbres="ALA A 317 " segid="A "
> pdbres="NAG A 401 " segid="A "
> Not linked:
> pdbres="NAG A 401 " segid="A "
> pdbres="NAG A 402 " segid="A "
> bond proxies already assigned to first conformer: 4309
> Chain: "B"
> [...]
> Chain: "C"
> [...]
> Residues with excluded nonbonded symmetry interactions: 26
> residue:
> [...]
> Number of atoms with unknown nonbonded energy type symbols: 3
> "ATOM 5046 HO4 NAG A 401 .*.A H "
> "ATOM 6215 HD22 ASN B 74 .*.B H "
> "ATOM 10057 HO4 NAG B 401 .*.B H "
> Time building chain proxies: 4.05, per 1000 atoms: 0.36
>
>
> Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do
> the trick - as I explicitly want to refine hydrogens I reckon they are
> added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to
> NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link
> instead of using the BETA1-4?
>
> Thanks again!
>
> B
>
>
>
> 2014-06-12 2:12 GMT+02:00 Nathaniel Echols <nechols at lbl.gov>:
>
> On Wed, Jun 11, 2014 at 5:05 PM, Benjamin Stauch <bs448c at gmail.com> wrote:
>>
>>> I want to refine a model that has two NAGs linked to an Asn - the sugars
>>> are already part of my initial coordinate file, but upon refinement the
>>> link between the NAGs gets lost. I have defined a cif_link file as follows
>>> that I load (using the GUI),
>>>
>>> apply_cif_link {
>>> data_link = "NAG-ASN"
>>> residue_selection_1 = "chain A and resname NAG and resid 401"
>>> residue_selection_2 = "chain A and resname ASN and resid 74"
>>> }
>>> apply_cif_link {
>>> data_link = "BETA1-4"
>>> residue_selection_1 = "chain A and resname NAG and resid 401"
>>> residue_selection_2 = "chain A and resname NAG and resid 402"
>>> }
>>>
>>
>> Okay, I think this may be part of the problem - you are missing the outer
>> "scope" for these parameter blocks, so they are not processed correctly.
>> If you change "apply_cif_link" to
>> "refinement.pdb_interpretation.apply_cif_link" in both places it may fix
>> the problem.
>>
>> Refinement doesn't crash or produce errors as far as I can see, however
>>> when checking the MolProbity output after refinement, it complains of
>>> missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant)
>>>
>>
>> Sorry, this is actually my bug (those atoms should not be included in
>> covalently linked sugars), and I think I still have an email complaining
>> about this in my inbox from late 2012. I need to overhaul that bit of code
>> anyway so I will see if Nigel and I can come up with something smarter.
>>
>> -Nat
>>
>
>
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