Re: [phenixbb] refining sugars

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:

...

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

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-- 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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-- 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