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

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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 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