search

pylelab / USalign

Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins
https://zhanggroup.org/US-align/
Other
103 stars 24 forks source link

Intermediate results output #1

Closed TimSkvortsov closed 2 years ago

TimSkvortsov commented 2 years ago

Hi, I was wondering if an option to save intermediate results could be added. For example, having the distance matrix from the all-against-all pairwise structure alignments (the one in Supplementary Figure 13 (a) of the US-align paper biorXiv preprint) would be very useful.

In addition, would it be possible to add a little bit more information about different --outfmt options?

Thank you!

kad-ecoli commented 2 years ago

I have just added option -full T for all-against-all pairwise alignment result in multiple structure alignment. You can use it as follow:

USalign -dir chains/ list -suffix .pdb -mm 4 -full T
TimSkvortsov commented 2 years ago

Many thanks, that's perfect! I have a quick question about MSTA: each pairwise alignment generates two TM-scores, what TM-score is used for the construction of the pairwise distance matrix for MSTA?

kad-ecoli commented 2 years ago

The one normalized by the shorter structure.

TimSkvortsov commented 2 years ago

The one normalized by the shorter structure.

Thanks!