On 04/26/2013 12:29 PM, Eleanor Dodson wrote:
Is there any consensus about the accepted format for this?
I believe Garib uses LINKR to add a link name to the record, (cant
find a description in the documentation though???)
but also in the documentation REFMAC is said to provide a link
between symmetry related like this
with the target distance here
LINK 1 P DG A 1 1.61000 O3' DC A 2
1555 6554
i
But REFMAC a) ignores the given distance and b) writes it out as :
LINK P DG A 1 O3' DC A 2 1555
2554 1.48
This is in agreement with the PDB definition but with a wrong distance
- presumably derived in the innards of the dictionary:
PDB LINK definition
12345678901234567890123456789012345678901234567890123456789012345678901234567890
LINK O GLY A 49 NA NA A6001 1555 1555 2.98
LINK OG1 THR A 51 NA NA A6001 1555 1555 2.72
12345678901234567890123456789012345678901234567890123456789012345678901234567890
LINK O GLY A 49 NA NA A6001 1555 1555 2.98
LINK OG1 THR A 51 NA NA A6001 1555 1555 2.72
coot seems to refuse to read the LINKR at all!
As for the last bit, do you mean 1) that coot gives a parsing error when
reading files with LINKRs or 2) that coot otherwise parses such files
OK, but skips past LINKR records (and in that case, what would you have
it do?) Which version of mmdb is the coot that you are using linked
against?
Paul.
