[phenixbb] NAG-NAG link definition seems to have no effect
Benjamin Stauch
bs448c at gmail.com
Thu Jun 12 11:20:16 PDT 2014
Hi Nigel,
many thanks -- that was indeed the problem, I should have thought of this.
But no more errors or drifting NAGs! Awesome
Ben
2014-06-12 17:37 GMT+02:00 Nigel Moriarty <nwmoriarty at lbl.gov>:
> Ben
>
> When you are running refinement in the GUI are you "adding hydrogens"?
> This will be adding the 3 hydrogens that are the problem. Clearly, it
> should be smarter but if you have the hydrogens you need in the input you
> can uncheck the add hydrogens.
>
> Nigel
>
>
> On Thu, Jun 12, 2014 at 1:55 AM, Benjamin Stauch <bs448c at gmail.com> wrote:
>
>> 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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>>
>>
>
>
> --
> 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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