Comments (4)
you can increase -Neff to downweight the crosslinks (see the influence of this in the supplementary figures of the alphalink paper) or remove msa subsampling altogether. Alternatively, you can change the fdr number on the crosslinking restraints or flatten the shape of the distribution. Finally, you can run multiple times with subsets of restraints. I also encourage you to carefully look at the crosslinking MS data to ensure error thresholding is done properly.
from alphalink.
Great! thank you so much! I'm trying these ways to see how it looks.
Thanks.
Yan
from alphalink.
Hi,
Running multiple times with subsets of restraints would be a better solution in my case. Do you have any detailed workflow on it? will you use the restrained model as a new input for next subset of restraints? How do you filter the restraints as a subset?
Thanks.
Yan
from alphalink.
Hi,
This workflow is not implemented at the moment. What you could do is shuffle your links once they are loaded and pick a subset. E.g., like this (untested!):
np.random.shuffle(links)
subset = 0.8
links = links[:int(n * subset)]
Should be inserted here: https://github.com/lhatsk/AlphaLink/blob/main/predict_with_crosslinks.py#L292
To have more control over the subsets, it might make sense to partition beforehand and just use the newly created CSV files, if you want to filter/ iteratively add restraints.
from alphalink.
Related Issues (18)
- Wrong array shape when using single crosslink record HOT 1
- problem with model loading HOT 12
- CUDA stub file missing for cpu-only build HOT 1
- No MSA output - precomputed alignments called automatically HOT 3
- Request for an example folder HOT 1
- Request for training HOT 5
- Problem with Crosslinking data input HOT 12
- Inter-subunit crosslinking data HOT 2
- Run "python preprocessing_distributions.py --infile restraints.csv" but get an error HOT 4
- Running "predict_with_crosslinks.py" with "restraints.csv --distograms" gives the error HOT 6
- Alphalink install failed HOT 3
- Installation unclear HOT 1
- crosslinks need to be provided as comma separated, not space HOT 1
- FDR Description in Arg parse is potentially wrong HOT 3
- Issue with multimer HOT 3
- Save pkl files HOT 1
- hands-on protocol for contacts_to_distograms HOT 34
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from alphalink.