James Krieger
James Krieger
This might help: https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=4092
A possible fix could be to read the CHARMM DCDs into VMD and write out new ones. I think those can then be read into ProDy.
We already have combinatorial extension (CE) and Dali. There's also the option of using Biopython's pairwise sequence alignment for structural alignment. It's unlikely that we'll add many more. Which methods...
I was also thinking CE alignment is very slow and I made a pull request to speed it up by only taking Calpha atoms (#1480). It's not merged yet as...
There's also the functions buildMSA (and its wrapper alignSequencesByChain), which was developed with clustal programs in mind but could be used with any external program with some small tweaks. [Line...
I meant that we'd integrate ProDy with the OpenCADD wrappers perhaps. It's definitely a nice idea and hopefully someone can do something about it soon, but it's definitely not urgent....
It depends what you're trying to do. If you really just want pairs of structures and you want to handle multiple chains at the same time then alignChains is the...
The cealign update is now merged. Also that git clone command wasn't quite right anyway. I tested something similar and it didn't like it. Anyhow, you can now just do...
It may be that the process is too memory intensive and the Jupyter notebook can't handle it. Could you try using a terminal instead and see if that works?
You could maybe try running `top` or `htop` in another terminal and see how much memory it uses.