On 05/07/2018 15:00, Yoder, Marilyn wrote:
I'm having problems adding XYP (beta-xylose) to my glycosylation chain in a
plant protein.
Hello again Marilyn,
Having reflected on the problem, I hope that I can offer a bit more insight than "use the latest version" -
so here's another attempt.
As you may know, Coot uses the standard Refmac monomer library, which (amongst other things) contains a list
of descriptions of carbohydrate linkages in list/mon_lib_list.cif. As it sets up a refinement, Coot
compares pairs of monomers against this list of linkages, so that, for example, an (ASN, NAG) pair will use
the NAG-ASN link description, a (NAG, NAG) pair will use the BETA1-4 link description (and so on). I now
recall that while developing this module we discovered that the monomer library did not contain a link for
(XYP, BMA). Which meant that as the refinement was turned on, the XYP "rapidly wiggled away" (as you'd put
it). So I made a new link and added it to list/mon_lib_list.cif. Coot was happy again.
So my guess is that you are using a version of the monomer library for which the XYP-BMA link description
has not percolated through the necessary hoops (as it were).
Patch attached - you may need to dedos your dictionary - I did (not sure why).
Regards,
Paul.
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16787a16788
> XYP-BMA XYP XYPmol1 . BMA DEL-HO2 .
> bond_XYP-C1B=_BMA-O2
19058a19060,19101
> data_link_XYP-BMA
>
> 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
> XYP-BMA 1 C1B 2 O2 single 1.426 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
> XYP-BMA 2 C2 2 O2 1 C1B 111.800 3.000
> XYP-BMA 2 O2 1 C1B 1 H1B 109.470 3.000
> XYP-BMA 2 O2 1 C1B 1 C2B 109.470 3.000
> XYP-BMA 2 O2 1 C1B 1 O5B 109.470 3.000
>
> loop_
> _chem_link_chir.link_id
> _chem_link_chir.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
> XYP-BMA chir_08 1 C1B 2 O2 1 C2B 1 O5B both
> #
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