[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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