Another week of internship is upon me, and I just realized that I am more than halfway through. We had the Monday meeting and oh one thing I forgot to mention that during last Friday meeting, the lab I am working with (Parasol Lab) announced that they are open sourcing their planning library and I get to work on that too with my grad mentor starting this week. In my previous blog (last week), I left myself some work to do but before I could get into that, I decided to run another test example for the protein binding cases; this protein has 9 binding sites. This caused an issue: the skeleton was being duplicated, one skeleton was being generated for all 9 binding sites but we only need one since that is enough to give a picture of the free space in the protein. So, I got to work. I have included a picture of how the skeleton looks like before and after I edited the code.

Figures 1 & 2 (same): showing the energy single skeleton

Figure 3: showing the single clearance skeleton

For some reason, the code I worked on (pictures above) is giving me errors when I run it so I tried resolving that and that is not resolved even at the end of the week. I was also starting to feel under the weather so this week was very slow; it’s part of working and research I guess, and I am learning to deal with being less productive.