[PyMOL] Query about inserting ligand at preferred base pairs of DNA

Hello Team, I need help in inserting ligand to base pair in DNA. I have a drug molecule and want to insert in between the base pairs I am interested in ( it is 12-mer dsDNA). I tried to follow the tutorials but cannot find something where I can insert ligand into the custom DNA sequence I have

Re: [PyMOL] Pymol-Alignment Module

Hi Ecem - If I understand correctly, you first want to align on one set of residues and calculate their RMSD, then to calculate the RMSD for the remaining residues without moving the structures. This is straightforward using PyMOL's internal command line. ``` # Create two selections called "sel1

[PyMOL] saving info regarding protein-ligand interactions in the log

Dear Pymol users! I am using a multi-model pdb containing the 80 predicted docking solutions as well as the receptor (the both presented in each frame). I need to calculate all hydrogen bonds (and possible other interactions) observed in each frame (=docking solution)? I've already used pymol for t

[PyMOL] Pymol-Alignment Module

Dear Pymol community, I have a question about alignment module of Pymol. I have two different pdb ids and each have about 100 amino acid long. I would like to align the specific parts of these proteins and see both how the rest of the proteins and also these specific parts superimpose with each ot