Hi Matthew,
thanks for the thought.
Yes, I agree, that it is average whole lot of conformations. I am aware
of FEMs, it is great tool, but I got similar results as with Polder maps.
Modelling just the "main chain" and calling it Jeffamin, is also an
option I was considering. It is part of the question, how to do properly
for the PDB deposition. If I do just the Jeffamin "mainchain", it would
be effectively PEG library, but not named as PEG. I think that would be
confusing.
However, really treating it as aa residue with invisible sidechain is
interesting option. Our lab consensus is to keep the atoms, but reduce
occupancy to almost 0. I think, I could do that for the methyl groups in
Jeffamin.
Best regards,
Jan
On 8/19/22 11:42, Matthew Snee wrote:
Hi
It is likely that your density is a consensus of multiple different
jeffamines binding at different rotational orientations, so that at
2.6A the methyl groups are essentially averaged out, and therefore the
density may not exist to be found.
Phenix has a tool called "feature enhanced maps" which is designed to
reverse the flattening of weak features, but I find its important to
have the best possible phases (I.E most accurate model) before using it.
I suppose you could model jeffamine, and delete the methyl groups (I.E
treat is like a residue with an unresolved sidechain).
Cheers
Matthew.
------------------------------------------------------------------------
*From:* CCP4 bulletin board <[email protected]> on behalf of Jan
Stransky <[email protected]>
*Sent:* 18 August 2022 10:37
*To:* [email protected] <[email protected]>
*Subject:* [ccp4bb] Polymer ligand (Jefffamin) modeling in low
resolution maps
Dear all,
we have a structure at not the greatest resolution (~2.6A) of which
crystal was grown in crystallization condition with Jeffamin. In the
maps, we see typical PEG-like sausages. Jeffamin is basically a PEG
decorated with some methyl groups and it is terminated with amine groups.
Now, the question is how to interpret such blobs? To my understanding
the methyl decoration is not regular, and it is not obviously visible in
the maps. Nor is clear, if there is a contact to the amine group. When
we tried to put in PEG models as placeholders, it explains the density
fine, but the contacts are nothing great, e.g. position of the oxygens
in the polymer is not clear.
Calculating Polder maps does not clear things up.
How would you deal with interpretation such maps?
Thank you for your ideas :-)
Jan
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