On 22/11/2023 14:02, Keitaro Yamashita wrote:
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Great, you are using the very latest CCP4 (with the latest monomer
library). I suppose Refmac properly identified the "ALPHA2-3" link
which should also appear in the PDB header (LINKR).
Using Coot, I just tried PDB 2osx which includes the ALPHA2-3 link
between GAL (B/2) and SIA (B/3). As you mentioned, it didn't work.
debug:: find_glycosidic_linkage_type() for B 3 SIA,B 2 GAL returns
"ALPHA2-3"
DEBUG:: make_other_types_of_link() "ALPHA2-3" for [spec: model 1 "B" 3 "" " C1 " ""] [spec: model 1 "B"
2 "" " C3 " ""] detected
DEBUG:: make_other_types_of_link(): now making a link restraint [spec: 1 "B" 3 ""] [spec: 1
"B" 2 ""] with type ALPHA2-3 and order switch 0
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0
debug:: find_glycosidic_linkage_type() for B 3 SIA,B 1 BGC returns ""
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 0
debug:: find_glycosidic_linkage_type() for B 1 BGC,B 3 SIA returns ""
Made 0 CHO-SS-and-other bond restraints
Made 0 CHO-SS-and-other angle restraints
Made 0 CHO-SS-and-other plane restraints
Made 0 CHO-SS-and-other trans-peptide restraints
It actually found the ALPHA2-3 link (but between C1 and C3? it's
strange..) and finally it didn't add any restraints. Paul, could you
please look into this?
Hi Keitaro,
When I was looking at carbohydrate linking (quite a few years ago now),
the SIA links were deliberately omitted because there was a bug (or
more) in the monomer library.
It seems that it is now time to revisit SIA linking. I'll add it to the
list now.
Regards,
Paul.
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