Changjian Feng

To improve the Uni-Fold structural modeling on Colab, which parameters should be changed, and range of the numbers? max_recycling_iters: num_ensembles: manual_seed: times:

Running clustered msa on Local ColabFold

1

The predication by AF takes a long time, for a longer sequence. And the run can be disconnected. How can we run our local colabfold using the clustered msa?

I tried to generate clustered a3m from the a3m file in the attachment [nNOSoxyFMN_relaxed_4e4bb.zip](https://github.com/user-attachments/files/17874469/nNOSoxyFMN_relaxed_4e4bb.zip); it is of a homodimeric protein complex. However, the generated EX files only have one protein;...

Four data files were generated after CPPTRAJ analysis: evecs.dat (Evecs file): myEvecs %eigenvec.dat (Standard Data File): XEVAL_00007[Frac] XEVAL_00007[Cumulative] XEVAL_00007[Eigenval] project.dat (Standard Data File): Mode1 Mode2 Mode3 helices.nmd (NMwiz output) How...

random seeds

2

For procedure 6 (local run to generate alternative conformations), can we use --num-seeds of 16 instead of the random seeds (0,...., 16)? On ColabFold webpage, num-seeds is recommended to use,...