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How long should it take to cluster Uniref?

The mmseqs2 code should be specifically compiled and optimised for your system. mmseqs2 optimisation is automated and might be available via Spack* (I'm not sure its actually done for mmseqs2), it is ...
M__'s user avatar
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How long should it take to cluster Uniref?

When I want to estimate the time taken to do something big, I subset my input data to something that takes a few minutes or less, and calculate forward from there. If there's alignment involved, it's ...
gringer's user avatar
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BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure

OK , visualizing both proteins in PyMOL , using set cartoon_gap_cutoff = 0 , I get : Apparently the two conformations , have more than one difference in various ...
pippo1980's user avatar
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2 votes

If I modify a PDB file with a specific mutation, how to minimize energy?

The previous answers suggest Chimera and FoldX, which require a license for commercial use. Commercial users can use pdbfixer or a similar tool to perform mutations (using e.g. applyMutation in the ...
Maximilian Press's user avatar
1 vote

Downloading a list of all RCSB-PDB entries

Did you try RCSB sequence similarity search? These two announcement highlight the options you ask about: Improved Searching with New Sequence Identity Cutoff (2017) Remove Redundancy in Search ...
marcin's user avatar
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