Jade Shi
Jade Shi
Hi, possibly a very dumb question here, but I was running through the T4-lysozyme / p-xylene example, and I noticed that when I load the receptor PDB and ligand mol2...
Hi, I was wondering what would be the best way to combine two models that had shared Monomer names. The reason I want to do this is I'm trying to...
Hi, I'm trying to align a pair of pdb/mtz files using the phenix.superpose_maps function and I was wondering if there was a way to fix the positions of one structure,...
Hi, Wondering if it would be straightforward to allow for non-protein cofactors to be considered in addition to the protein components when, for instance, predicting a new interface using masif_site?...
Hi, I'm running into a very strange issue when trying to model a second order reaction that contains only one species, wondering if I could get some help. Specifically, I'm...
... application of AtomIndices.dat Generators were mistakenly screened with AtomIndices.dat, when all atoms from generators should be used. This fix sets the atom indices attribute to the 'metric' object to...
Hey guys, I've been trying to develop a way to calculate an accurate metastability for a kinetic intermediate state in my protein system, and I came up with I think...
The script calculates state populations by calling msm_analysis.get_eigenvectors and requesting only one eigenvalue. I found that this leads to non-convergence issues. Increasing the number of requested eigenvalues (i.e. >= 4)...
Hi, I recently noticed 2 potential bugs in the TPT function of MSMExplorer: - Comparing the top pathways generated by MSMExplorer to those found with tpt.py, I see a divergence...
Hey, I was wondering if it might be worthwhile to give the PCCA.py script an option to only output MacroMappings.dat, and thus only require a transition matrix as an input....