Re: [ccp4bb] Problem of data reprocessing with XDS

Hi John, good idea in principle, but the amount of incompatible code changes between versions is surprisingly large. On top of that, XDS philosophy has always been that there is a single "best" algorithm (which may be fine-tuned in subsequent releases). The main arguments for that are: - it is

[ccp4bb] 3D classification of a small membrane protein.

Dear all I have a question about the 3D classification of a membrane protein using Relion 3.1, where I aim to remove some junk particles. The protein is relatively small (180 kDa), and its structure has already been resolved by cryoEM. It has minimal features outside the micelle ring and is primar

Re: [ccp4bb] Problem of data reprocessing with XDS

Hi Kay, thank you so much for the explanation, this is very helpful. Maybe it is already possible, but perhaps the user could select whether to do the background estimation using either the old or new way (with or without local fitting), via the XDS.INP file? Thanks again, John On Sat, Oct 5, 202

Re: [ccp4bb] AlphaFold3

Hello, I would like to take this opportunity to announce the release of our new web-tool, FoldScript (https://foldscript.ibcp.fr/), which complements our web-tool ESPript. FoldScript allows to analyze and to filter with experimental results (ie residues known to be involved in intermolecular in

Re: [ccp4bb] Problem of data reprocessing with XDS

Dear John, version 202406030 of XDS estimates the background "under" a reflection in a different way than 20230630 and earlier. The new way uses a background template based on the background image constructed in the INIT step of XDS, whereas in the old way that was only used for calculating a s

Re: [ccp4bb] AlphaFold3

Dear Jon I did the same for a dimer of a structure we just solved but only now writing the paper. AF3 predicted the monomer to an RMS of about 0.3 and dimer to about 0.5 Angstroms Structure not yet in the PDB, but soon Joel Sent from my iPhone On Oct 5, 2024, at 17:35, Jurgen Bosch

Re: [ccp4bb] AlphaFold3

I used it for PPI prediction of a mAb and our target protein and it was surprisingly accurate compared to our crystal structure. Binding of the mAb was <0.5 rmsd I was stunned. Jürgen P.S. paper should be accepted soon, but you’ll find a current version on BioRxiv if you are interested. AF3 is not

[ccp4bb] AlphaFold3

Just wondering if anyone has any comments on, or concrete experiences with, alphafold3. I might try to cobble something together for Crystallography News (he says, having missed the main Nature paper, ahem). My googling has only given me hype and gripe so far ;-0 ;-0 Best wishes, Jon Cooper. jo

Re: [ccp4bb] Problem of data reprocessing with XDS

Dear Kay, do have any more information or would you mind explaining a bit more what changes in the XDS code led to these significantly different statistics in the different XDS versions? Thanks,John On Wednesday, October 2, 2024 at 02:35:25 PM CDT, Kay Diederichs wrote: Dear Yimin,