-
In setting up a variety of systems for simulation I came across one with a thioether bond (something I haven't encountered before in a protein I'm trying to simulate). The PDB structure is https://www…
-
Make a toggle, provide it on a per-tab basis?
Also elucidate how edge cases should be handled to make sure the end-to-end pipeline is working correctly
-
Hi,
I am trying to build a coarse-grain system that has a lipid, sodium, and protein, but it seems martinize doesn't recognize lipid molecules (POPC/POPE) and sodium ions.
The command I used:
…
-
is it possible to have a modification that adds an additional bead to the given residue? Eg. if we have a phosphoserine, we can't give a single letter aa code in a fasta file, but could use the `-mod`…
-
I tried running GeoDock with a VH-VL antibody complex + its protein antigen. GeoDock succesfully generated a docked structure, but it looks like the antigen is bound on the opposite side of the VH-VL …
wjs20 updated
9 months ago
-
Hi,
Based on the documents NeighborSearch class can find neighbor for residues, Could someone help me how? Because if I start from a residue it does not have coordinates to find its neighbors. So I w…
FH96 updated
8 months ago
-
Hi, tks for making this repo public and documented.
I have a couple of questions
1. In `J.1. Training details` you outline the filtering protocol used to reach the final training set. Would it be…
-
I created unpaired and paired MSAs using jackhmmer searches and created two separate MSA contexts out of them. However, when you combine protein complex modeling with a ligand, the AllAtomStructureCon…
-
Structmap currently runs off residue numbers, and ignores inserted residues. Need to adjust this, and find a better way of determining the protein sequence for each chain.
-
Hello,
I happily use the residue stepper command (`isolde step` or shorthand `st`) all the time, it's very convenient. I have two suggestions that could make its use even nicer when using it repeat…