Hi,You can also use Theseus (https://theobald.brandeis.edu/theseus/) to superimpose the NMR states using maximum likelihood.By running:theseus 4hiq.pdbit will spit out the superimposed ensemble and also the average structure which you can use as a guide to trim the flexible bits. That resulted in a TFZ of 6.4 against the 4ey9 data in Phaser (2h run). The Alphafold predicted model performed significantly better, Phaser found a solution with a TFZ of 10.7 in a couple of minutes.Thank you for all the excellent suggestions. (And the aligned models!)I am not ACTUALLY trying to solve the structure - it is insulin, which I have seen before..It was a student project - solve 4ey9 using 1hiq.. which didn't work in a straightforward way. Hence my puzzlement..Insulin MR is never easy - there is only 30% solvent, metal ions not in the model, two molecules in the asymmetric unit, each with two chains to position,and several different folds to choose from in the PDB (would be interesting to see what Alphafold predicts from sequence alone..)To add to the difficulty - the strong low resolution data for 4ey9 is missing which is never good for MR either.Will try to rationalise what I have learnt.EleanorTypically we only align regions within a certain rmsd for backbone heavy atoms since regions lacking NOE’s are just randomly placed. The aligned regions should be listed in the original manuscript in their statistics table. You can just make these selections in pymol to get the best alignment. We used to use a program called MolMol
Best,
Linda
From: CCP4 bulletin board <[log in to unmask]> on behalf of Randy John Read <[log in to unmask]>
Date: Thursday, March 2, 2023 at 10:19 AM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [ccp4bb] NMR structiresATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
Hi Eleanor,
Normally they are aligned, but I guess not for really old ones.
I tried to use Ensembler to align them, but it uses SSM, which didn’t find enough to work with I guess. However, ChimeraX’s matchmaker tool did manage, and you can see the ensemble isn’t very tight!
Randy
On 2 Mar 2023, at 15:09, Eleanor Dodson <[log in to unmask]> wrote:
I have been looking at 1hiq - an NMR structure with 20 models.
I had always assumed that an attempt had been made to overlap the first with the second, third etc, but this does not seem to be so for this structure..
Have I been labouring under a misapprehension?
Eleanor Dodson
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Randy J. Read
Department of Haematology, University of Cambridge
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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1--Ricardo PaduaHHMI Research SpecialistKern Lab