helen-louise (baratron) wrote,

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Haven't written anything here for ages. Been kinda busy :) I have a desk in the Postgraduate Student Office at college, and a key that allows me to physically access a room with a Big Computer in. Finally got access to all the computers I need to use, and have been teaching myself how to use the software. I've been finding out how to do things that aren't documented in the manuals, and feeling quite clever for working it out.

I have a rule that I Will Not read livejournal/deadjournal from work, except in an emergency (urgent need to contact someone specific). Partly this is a security thing - the computer on my desk only has Internet Exploder 6 (yes, really), and I don't have permission to install anything less insecure. Partly it's to avoid the slippery slope where "I'm at work, so I must be working"; 2 hours later, still browsing the interwebs. I need to find out how to post to lj via email, because there have been a few things that I'd have liked to shoot off as quick posts in the middle of work.

My next problem is prioritising my work. At the moment I have several projects that are time-consuming, and I'm not sure what order to do them in. I need to:
  • finish the GOLD tutorials (1-2 hours)
  • finish making notes on GOLD from the manual (2-4 hours)
  • make a load of notes on molecular modelling, with specific reference to genetic algorithms, from the modelling textbook o'doom (?? absolute guess, 20 hours? gods only know, really. But it'll be a while because it involves MATHS.)
  • write up my notes on protein synthesis (5-10 hours? I understood it all, eventually, it's just a case of how neat I want to make things.)
  • write up all the lectures I've attended in the protein folding classes (as long as a piece of string? uh... each lecture will take 2-4 hours to write up, longer if I consult the speaker's publications as I'll have to find them online and download them, and I've been to 7 of the 10 lectures so far. But I won't bother to write up the lectures that didn't mean a lot to me, such as the one in which all I learnt was "all of the textbooks currently in existence are wrong". So let's say 5 lectures x 5 hours as an absolute limit, and get 25 hours)
  • find the correct crystallographic structures online for the protein I'm supposed to be using (1 hour, probably sitting in Philip's office. Not hard.)
  • remove the ligands from the crystallographic protein structures (minutes) and define the protein binding site (uhh...)
  • read all of the relevant papers about the Hsp90 binding site to make sure I get all the essential parts in! (30 minutes to many hours. I already know that there are 3 key hydrogen bonds, and could find a paper within minutes to confirm which residues are involved in those. But are there any other important quirks? Not sure.)
  • make sure each protein binding site has the correct shape and all residues have the right tautomeric and protonation states (How long is a ROPE?)
  • learn how to use whatever piece of software we're going to use to draw our ligands (no more than 5 hours)
  • draw the ligands (20 minutes per ligand)
  • optimise all the bond angles, conformations and energy states of the ligands (impossible to say. I have no idea how long the calculations would take.)
  • dock the new ligands into the various protein binding sites (5 minutes per protein-ligand combination)

Clearly some of these things have to be done before some other of these things, that's easy enough. But I don't know what order to put the, er, groups of work into. I can't make a timetable where I work on something for a couple of hours then switch - that doesn't work with the whole being bipolar thing. (I can either concentrate, or not concentrate, there is no middle ground. If I am failing to make any headway at all on a project then I can switch to another piece of work and possibly even do very well at it; but if I am in the middle of work and highly focused, I can't switch to something else and expect to be able to get anything done. I believe this is similar to what some people experience with ADHD, but the meds that help with ADHD are totally contraindicated for bipolar).

Tags: research

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