freenode/#clasp - IRC Chatlog
Search
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.
10:41:08
frgo
::notify drmeister Thanks again for fixing the clbind thing. Most of it works now. I have one case where I am running into a road block - I will ask you again later on that.
14:05:52
Colleen
drmeister: frgo said 3 hours, 24 minutes ago: Thanks again for fixing the clbind thing. Most of it works now. I have one case where I am running into a road block - I will ask you again later on that.
14:07:33
scymtym
beach: i'm experimenting with using CST:RECONSTRUCT in ECLECTOR.CONCRETE-SYNTAX-TREE:CST-READ to improve precision for e.g. reader macros. it seems to work ok so far. does that sound like a good idea to you?
15:02:31
beach
I had lunch guests today, so I spent all morning cooking, and all afternoon washing dishes and discussing with my guests.