Hi David Briggs,
Thank you for the suggestion of AceDrg. I gave it a try, using the Coot way
and the Jligand way for AceDrg. For some reason the Coot method didn't make a
cif, only jligand did. But the cif didn't have any effect on refinement. What
did work for Phenix was to define the
Hi Joel,
That's a great idea! I've considerd it, and technically it would work as you
suggest to refine correctly. However, that would look like more carbons come
from one of the two precursor molecules than the other, which chemically would
be wrong. I really want to avoid giving the
Hi David,
Rob Nicholls gave a talk about AceDrg and link generation at a CCP4 SW a few
years ago..
https://www.youtube.com/watch?v=p4oTJ0bjD3M
I think this will contain the answers you are looking for.
Cheers,
David
--
Dr David C. Briggs CSci MRSB (he/him)
Principal Laboratory Research
Hi,
Not looking deep at your sequence/link, have you tried to move the link to a
single bond and avoid the double as the linked bond? This way you can
paraetrise the double bond correctly. Not sure is global phasing could help..
Joel
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Hi Learned Friends,
I'm trying to refine a structure that has a very similar staple to the one in
8GJS. In that structure, there's a double bond between residue 5 and 12 in
chain B. I've tried to define a link using
