10:15 am — 11:15 pm
Paperwork
- working on essay for Burroughs Wellcome application.
Chromatin Imaging
- Testing IR shutter for 750 imaging
- wrote new communications/connections file for Toptica laser, saved to desktop for quick use
Toptica750.ht(previous file copied from old storm2 computer doesn’t work — com port changed).
- wrote new communications/connections file for Toptica laser, saved to desktop for quick use
- taking bead data
- setting up to image new samples: L4E02-647 + E01-750
- 647 worked much better this time — bright clear spots obvious in every cell.
- 750 spots look pretty dim
- originally made with pure BME buffer, spots were dim. Remade with MEA buffer, maybe a touch brighter but not strongly so. Remade with brand new MEA buffer, still not a dramatic change to 750 brightness.
- original region selected went outside buffer resevoir over edge of PDMS. spots equally bright here (they were still bathed in buffer) but switching is poor (no buffer turn-over).
Python
- working to get KnotAnalysis running on Odyssey (requires linux)
- see emails from today’s date from RC computing with directions for running anaconda python and installing local python packages
- Adding my directories to systems path once in python:
import sys, thensys.path.append("/n/home05/boettiger/OpenMM/openmmPolymer") - KnotAnalysis seems to execute fine, though the number doesn’t quite make sense (200 monomers “simplified” down to 32 but with a knot number (crossing number) of 427.3 something like that. Why isn’t this an integer and how can it be substantially larger than the number of simplified monomers (or total monomers?)