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21:39:22
DVSSA
How do I start cando/clasp? I think it built correctly (last line from build.log 'install_cboehm' finished successfully). Typing clasp/cando in terminal does nothing.
21:44:21
drmeister
That provisioning script I gave you is for building cando - there are dockerfiles that you can mine in clasp/tools/dockerfiles that show you how to provision a machine for jupyter notebooks or slime.
6:33:53
frgo
I just woke up. And I still have problems building my extensions. The scraper is behaving differently than two weeks ago. I don't know why yet.
6:44:48
frgo
Found the problem. 6 hours of sleep abd a fresh look onto the problem and voilĂ - solved.
7:16:00
drmeister
That is a generated molecule superimposed and then forced into the "pose" of a similar molecule in the active site of thrombin.
7:18:04
drmeister
This is for a "free energy perturbation calculation". It involves building molecules that are similar to each other but differ in two different groups that chemists can modify.
7:19:03
drmeister
The built molecules need to be positioned in the active site of the protein in the same pose as a "template" molecule that was mixed with the protein and the complex structure solved using X-ray crystallography.
7:19:38
drmeister
The trick here is to programatically build different candidate molecules and superimpose them on the template molecule and force them into a similar "pose".
7:25:03
drmeister
This is neat as well - all of the candidate molecules in the correct pose - but arrayed on a grid.