Since the publication of #AlphaFold2 and #RoseTTAFold and now that the tools and models have been made accessible, there has been an avalanche of attempts to solve old crystal structures. This thread covers tips from the #PhaserTeam for doing #MR with these models. (1/...)
The first thing to be aware of is that the B-factor fields contain measures of confidence in the correctness of the prediction, not actual B-factors. This means: 1) we can use that confidence to trim the model and 2) we need to convert that to an appropriate B-factor. (2/...)
Phaser will take those B-factors and use them to weight the different parts of the model. This can improve your chances of success with the model. (3/...)
If your model comes from the #RoseTTAFold server, it will have an estimated rmsd error in A in the B-factor column. They already give the option to obtain versions of the model from which atoms with an error estimate over some value have been trimmed. (4/...) Image
For #MR in #phaser you should process the #RoseTTAFold model. From the latest nightly build from #phenix, you can use our tool phenix.voyager.rmsd_to_bfactor to process those error estimates to B-factors and also optionally trim the model. (5/...)
If your model comes instead from the #AlphaFold database at the #EBI, or from their Colab notebook, the metric on their B-factor column is the LDDT. This is the score that is shown as quality metric, and is a percentage with 100% being best. (6/...) Image
@RandyJRead has done some exploration of how LDDT empirically relates to RMSD, and with that and our previous formula to convert from RMSD to estimated B-factors, now we also have a small tool, phenix.voyager.lddt_to_bfactors available in the most recent nightly build. (7/…)
You really want to process the #AlphaFold models, because if the LDDT scores are treated as B-factors, the best parts of the model will get the lowest weight in the #MR calculation! (8/..)
@sokrypton was kindly told me that if you run #RosettaFold locally or in a notebook the LDDT will be in the range from 0 to 1 instead of 0 to 100, so we will update our script to deal with that too. I'll keep you posted! (9/...)
Also @BenButt2 has told me locally run AlphaFold models will have an empty bfactor column and the IDDT will be on a different file!
The tool was updated to check if lddt is in percentage or fractional form. You can find on the very latest phenix nightly builds available on phenix-online.org/download/night…. Even if tagged as incomplete on some platforms they will work on the others. PM me if issues!

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Claudia Millán

Claudia Millán Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us on Twitter!

:(