[phenixbb] N-linked glycans in phenix.refine

Engin Ozkan eozkan at stanford.edu
Wed Sep 30 07:53:09 PDT 2009


Hi Jose,

I haven't come across that error. Maybe Pavel will recognize it. Working 
with an NAG with O1 deleted should be OK, that's what I always do as well.
A friend had an O1 deletion error before; his solution was to upgrade 
phenix. It would be great to do that now, since the last stable version 
(1.5-2) was released yesterday, so that would be my suggestion.

You can also post how you define your restraints in your parameter file 
for others to check...

Engin

On 9/30/09 3:41 AM, Jose Casasnovas wrote:
> Thanks so much for the update.  You were right.
> Now I have another problem, maybe you know.  I am
> using a NAG without the O1 and the program is trying to delete and stop
>
> RuntimeError: delete_atom_in_place: unknown atom_id: O1
>
> Do you know how to avoid this?
>
> Jose
>
>
>
>
> At 20:22 29/09/2009, you wrote:
>    
>> That's because there is no such data link as NAG-NAG-B-D. Instead, you
>> should use a BETA1-4 link. This is similar to what CNS used, if you are
>> familiar with that (I think it was B14 in CNS).
>> If you want to know where all the phenix link definitions are, type
>>
>> phenix.where_mon_lib_list_cif
>>
>> and read the file that's listed.
>>
>> It is good to read this to know which residue selection is selection_1
>> and which is selection_2. In it you'll see this or something like this.
>>
>> data_link_BETA1-4
>> #
>> loop_
>> _chem_link_bond.link_id
>> _chem_link_bond.atom_1_comp_id
>> _chem_link_bond.atom_id_1
>> _chem_link_bond.atom_2_comp_id
>> _chem_link_bond.atom_id_2
>> _chem_link_bond.type
>> _chem_link_bond.value_dist
>> _chem_link_bond.value_dist_esd
>>    BETA1-4  1 O4      2 C1        single       1.439    0.020
>> loop_
>> _chem_link_angle.link_id
>> _chem_link_angle.atom_1_comp_id
>> _chem_link_angle.atom_id_1
>> _chem_link_angle.atom_2_comp_id
>> _chem_link_angle.atom_id_2
>> _chem_link_angle.atom_3_comp_id
>> _chem_link_angle.atom_id_3
>> _chem_link_angle.value_angle
>> _chem_link_angle.value_angle_esd
>>    BETA1-4  1 C4      1 O4      2 C1      108.700    3.000
>>    BETA1-4  1 O4      2 C1      2 O5      112.300    3.000
>>    BETA1-4  1 O4      2 C1      2 C2      109.470    3.000
>>    BETA1-4  1 O4      2 C1      2 H1      109.470    3.000
>> loop_
>> _chem_link_tor.link_id
>> _chem_link_tor.id
>> _chem_link_tor.atom_1_comp_id
>> _chem_link_tor.atom_id_1
>> _chem_link_tor.atom_2_comp_id
>> _chem_link_tor.atom_id_2
>> _chem_link_tor.atom_3_comp_id
>> _chem_link_tor.atom_id_3
>> _chem_link_tor.atom_4_comp_id
>> _chem_link_tor.atom_id_4
>> _chem_link_tor.value_angle
>> _chem_link_tor.value_angle_esd
>> _chem_link_tor.period
>>    BETA1-4  BETA_1   1 O4     2 C1     2 C2     2 C3        0.00  20.0 1
>>    BETA1-4  BETA_2   1 C4     1 O4     2 C1     2 C2        0.00  20.0 1
>>    BETA1-4  BETA_3   1 C3     1 C4     1 O4     2 C1        0.00  20.0 1
>> loop_
>> _chem_link_chir.link_id
>> _chem_link_chir.atom_centre_comp_id
>> _chem_link_chir.atom_id_centre
>> _chem_link_chir.atom_1_comp_id
>> _chem_link_chir.atom_id_1
>> _chem_link_chir.atom_2_comp_id
>> _chem_link_chir.atom_id_2
>> _chem_link_chir.atom_3_comp_id
>> _chem_link_chir.atom_id_3
>> _chem_link_chir.volume_sign
>>    BETA1-4    2 C1      1 O4      2 O5      2 C2      positiv
>>
>> Engin
>>
>>
>> On 9/29/09 10:44 AM, Jose Casasnovas wrote:
>>      
>>> Dear Phenix users.
>>> I am trying to refine N-linked glycans in phenix.  The Asn-NAG link
>>> appears to be recognize by the program, but the NAG-NAG link is not.
>>> I guess the cif_link must be missing.
>>>
>>>
>>>     Monomer Library directory:
>>>        "/home/soft/phenix/phenix-1.4-3/ext_ref_files/mon_lib"
>>>      Total number of atoms: 8947
>>>      apply_cif_link:
>>>        data_link: NAG-ASN
>>>          mod_id_1: DEL-O1
>>>          mod_id_2: DEL-HD22
>>>        residue_selection_1: chain N and resname NAG and resid 5161
>>>        residue_selection_2: chain E and resname ASN and resid 516
>>>      apply_cif_link:
>>>        data_link: NAG-NAG-B-D
>>>
>>> Sorry: Missing CIF link: data_link_NAG-NAG-B-D
>>>      Please check for spelling errors or specify the file name
>>>      with the link as an additional argument.
>>>
>>> How can I get the required cif_link file and where to place it??
>>>
>>> Any suggestion.
>>>
>>> Thanks.
>>>
>>> Jose
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>        
>>
>> --
>> Engin Özkan
>> Post-doctoral Scholar
>> Howard Hughes Medical Institute
>> Dept of Molecular and Cellular Physiology
>> 279 Campus Drive, Beckman Center B173
>> Stanford School of Medicine
>> Stanford, CA 94305
>> ph: (650)-498-7111
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>      
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>    


-- 
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111




More information about the phenixbb mailing list