The purpose of this utility is to explore the sterics and symmetry of installing different DNA-binding domains within the porous scaffold crystals reported by the Snow laboratory.
Optional: Click here to populate fields below with demo values.
Step 1. Upload or fetch a model of your DNA-binding domain of interest.
Step 2. Pick the active protein chain(s). PDB entries often have multiple copies. For this next stage the goal is to trim away everything except one copy of your binding domain and a minimal length double stranded DNA (dsDNA). The first step is to pick just the one or two protein chains that constitute your binding domain. If you hover your mouse above a residue in the Mol* viewers it will tell you the chain and residue number.
Step 3. Truncate the DNA. The next step is to specify which DNA chains you want to retain for your minimal model. We provide a couple of ways to help you select a subset of the DNA residues. Often the easiest is to use the drag-and-drop selection.
When picking DNA be careful of non-canonical bases or missing bases, the goal is to retain a simple contiguous dsDNA.
Step 4. Check your Work. Once you have a selection of chains and residues, you can inspect those by pressing the Preview Selection button and make revisions as necessary.
Once your preview model looks correct, a nice complex between your protein chain(s) and the minimal dsDNA, proceed to Stage 2 below.
Note: the calculation will run in your browser, so this could be slow. Sometimes there is a pop-up warning that the page is frozen. In this case, we recommend the Wait option.