[phenixbb] refining sugars

Engin Ozkan eozkan at stanford.edu
Wed Sep 30 11:12:29 PDT 2009


I just answered Jose's question on this yesterday. The reason you are 
having trouble is that there is no NAG-NAG link. It is a BETA1-4. Read 
the post to see what data_link names are allowed, and use them for your 
sugars.

Below is a copy-paste of my post from yesterday:

>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 9/30/09 10:56 AM, Tirumala Kumar Chowdary wrote:
>  Thanks for the reply,
>
>  here is part of the log file, which shows the parameter input for nag
>  refinement
>
>
>  Monomer Library directory:
>     "/usr/local/phenix/phenix-1.4-125/chem_data/mon_lib"
>   Total number of atoms: 6260
>   apply_cif_link:
>     data_link: NAG-ASN
>       mod_id_1: DEL-O1
>       mod_id_2: DEL-HD22
>     residue_selection_1: chain C and resname NAG and resid 1670
>     residue_selection_2: chain A and resname ASN and resid 670
>   apply_cif_link:
>     data_link: NAG-ASN
>       mod_id_1: DEL-O1
>       mod_id_2: DEL-HD22
>     residue_selection_1: chain C and resname NAG and resid 1784
>     residue_selection_2: chain A and resname ASN and resid 784
>   apply_cif_link:
>     data_link: NAG-NAG
>     residue_selection_1: chain C and resname NAG and resid 1784
>     residue_selection_2: chain C and resname NAG and resid 1785
>   Number of models: 1
>   Model: ""
>     Number of chains: 3
>     Chain: "A"
>       Number of atoms: 5125
>       Number of conformers: 1
>       Conformer: ""
>         Number of residues, atoms: 681, 5125
>
>  I am presuming that it read what ever it needs to make the ASN-NAG
>  bonds and NAG-NAG bonds.
>
>  what am I missing here ?
>
>  Tirumal
>
>
>  Quoting Engin Ozkan<eozkan at stanford.edu>:
>
>>  You don't need to create cif files; phenix has them. NAG is definitely
>>  there, and you can have two NAGs linked by any biologically-relevant
>>  glycosidic bond you want. You need to define the links, however. I think
>>  posting the cif_link.params may get you more help.
>>
>>  Engin
>>
>>  On 9/30/09 8:49 AM, Tirumala Kumar Chowdary wrote:
>>>  Hi,
>>>
>>>  My question is related to the 'refining sugars in phenix' questions
>>>  that have been appearing on the bb for the last two days.
>>>
>>>  I am trying to refine my NAGs and somehow phenix is ignoring the sugars
>>>  in my structure. Neither it is making a bond between my ASN and NAG nor
>>>  NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly,
>>>  though.
>>>
>>>  I am using in version 1.4.125 still. Is this the problem ? Does
>>>  upgrading to any of the later build will help ?
>>>
>>>
>>>  Tirumal
>>>
>>>  _______________________________________________
>>>  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
>>
>
>
>


-- 
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





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