On 6/12/25 14:47, Leah Braviner wrote:
Hello Paul, Bernhard and Markus!
Thank you all for your responses - and sorry for the lack of context.
I am building/refining a crystal structure which contains a synthetic RNA that
was designed with the 5' phosphate group in tact. So far I have built with a
regular nucleotide string in Coot, but the 5' nucleotide in this case is given
a PO3 (presumably as the final O would come from the 'next' nucleotide, at
position -1).
Wait, what? I am confused. Is there a "not" missing in that sentence?
The "new" (as of 5(?) years ago) monomer library. Monomers now come with
linking atoms and care needs to be taken (by me, mostly I think) to
delete the linking atoms when monomers become parts of polymers.
Also, you say "PO3" - do you mean "OP3"?
My workaround has been to swap nt1 for a GTP ligand and then remove
individual atoms from the extra phosphates - it seems to work, but I'm slightly
concerned about different restraints for refinement/deposition?
You are right to worry.
Plus then of course the GTP gets flagged as having missing atoms.
Yes... I imagine you will have stripped off two off the phosphates...
This is not The Right Way...
I was sort of looking for an OXT but for nucleotides - unless I'm setting it
up wrong, OXT seems to work for the 3' end of the RNA but not the 5'
(presumably analogous to N vs C termini?).
No... All standard nucleotides have 5' phosphates (with 4 oxygen atoms,
I mean).
Alternatively, I did try adding an oxygen atom and creating a link but wasn't
sure exactly how to make a covalent bond such that the position can be refined
correctly. Markus, thank you for your suggestion to rename the OP3 I will try
that now.
As far as I can see the right workflow should "just work" - with no
extra thought or input from you (the user).
OK, so to test, do a Get Monomer for a "G" - and if the you don't see a
fully formed phosphate then something is wrong with your setup, or you
are using an ancient Coot and/or Monomer Library.
Paul.
########################################################################
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
