baratron: (science genius girl)
I'm feeling well enough to restart my PhD again this term. Spoke to Philip on Friday about changing my project to something more manageable with my physical limitations, and that actually went remarkably well. I'll write more about it when it's all been approved by the Graduate Committee.

There are various Things to deal with this term: the Graduate Symposium and the Retreat, both of which terrify me. I still don't know how exactly I'm going to get to Mill Hill for something that starts before 10 am, or how I'm going to manage for a whole day in a strange place without anywhere to go and collapse if necessary, but I'll work that out later. The Retreat is in Cambridge and involves an overnight stay, and is no doubt fully catered, which fills me with utter horror. I have a long-term phobia of Other People Controlling My Dietary Intake. It started when I was a teenage vegetarian and people thought I would eat chicken, or chilli with the pieces of meat fished out (eww). It's only got worse as I've developed quite genuine food intolerances. Traces of dairy make me really very unwell in the digestive department for an alarmingly long time.

Perhaps in preparation for this, I am doing something on Wednesday which terrifies me. They picked six random students and invited us to lunch with the visiting speaker at College. I'm not sure if it was random or if they looked for people whose work was vaguely relevant to hers. I wrote back and said that it isn't that I *can't* go, but that I have lots of food intolerances; but apparently there is no prebooked menu, and you can choose anything they sell. So I agreed to go because I've become way too good at avoiding things which make me anxious. At a time of mental health crisis, it's reasonable to avoid extra stress, but in the long term it isn't healthy - you can't get through life by avoidance.

I will no doubt regret this decision multiple times between now and Wednesday afternoon, but what is the actual worst that can happen? That there's nothing I can eat apart from a bit of salad and fruit? No one ever died from missing one meal! I have to keep my fears in perspective.
baratron: (test tube)
Philip & I leaving the postgraduate lab on Friday to "borrow" ice from the undergrad lab:

"Don't wear your gloves outside the lab."
"Oh!" *takes them off* "Er... why not?"
"Well, partly because you don't want to get whatever's on your gloves on door handles that people are going to touch with bare hands."
"Ah. That makes sense."
"Also because it freaks people out."
"Oh." *sadly* "I always thought that freaking people out was the fun part of being a scientist."
baratron: (science genius girl)
Today's PhD Comic actually made me laugh out loud for over a minute. (Here's a permanent link for anyone who reads this in the future).

Dear Philip, I love you dearly, but that PhD supervisor IS YOU!
baratron: (test tube)
Things that are incredibly embarrassing if you're a postgraduate chemistry student: When you show your results to your supervisor and he says "What stereochemistry did you use?", and you're left blinking and saying "Stereochemistry...?!". I totally forgot that inhibitor 1 (and by extension, 2) has a chiral centre! Oh dear. It turns out that I'd been working with the R- isomer, so now I need to go and repeat the molecular docking with the S- isomer. To be honest, looking at the results, I don't think that it'll make any vital difference - but it's still important to try both!

Results from today are exciting in a good way - they seem to be confirming that the method is valid. Philip & I had been mystified by a hydrogen bond that both PBD Ligand Explorer and GOLD were showing in the X-ray structure from the original research group. It appears to be linking an ether group in the ligand to the O=C of the residue Asn 51, which is strange because you can't have hydrogen bonds without hydrogen - but we didn't think that either the amide or the ether oxygens would get protonated at pH 6.5. The joy of having two supervisors is that when I showed it to Katherine, she suggested it could be tautomerism - something like keto-enol. I just looked it up and there's such a thing as amide-imidic acid tautomerism. I can't find anything more useful from a quick Google search, but I'll add it to the list of things to look up in the huge 11-volume heterocycle book OF DOOM.

I'm feeling a bit better emotionally today. It took me forever to settle down to work, but I've eventually got quite a bit done. Yay.
baratron: (rainbow chemistry geek)
So, you probably want to know how my college work is going. The thing is, nothing very exciting has happened. I mean, I spent the whole of last week reading books and making notes on protein synthesis. Wow.

So instead I should tell you more about the wonderful but utterly insane man who is my primary supervisor, Philip. Lately he has been working fairly intensely with an MSc student who took a month off work to get as much as possible of his lab project done (remember we're all part-time students?). Said student is lovely but very uncertain of himself in the lab. As a result, I've been getting regular text messages on my phone from Philip saying that he can't get to meetings because of "disasters in the lab". I have total sympathy and understanding because I will be exactly the same once I start lab work, having not done anything of that nature since, er, 1996.

Anyway, so I saw Philip on Tuesday and he apologised for having had to spend so much time with [other student]. I said "It's ok, I've mostly just been dealing with disability stuff. Actually, I've been quite amused by it all, because it's like building up credit - if you've had to deal with that many disasters with another student, you should be happy to deal with at least that many with me!". And I told him how Richard and I apparently have divergent ideas of what constitutes successful recovery of a lab situation. Personally, I'm happy if no humans or expensive equipment is damaged, and the product can be recovered. Richard thinks that only the equipment is important, because humans can heal and you can redo the work. I think that Richard is a big-ol'engineer and has no idea what a multi-stage chemical synthesis is like.

So I asked what has been happening. Philip said "You know we don't have an NMR machine, we have to go over to UCL to borrow theirs?".
I said "Yeeees?", picturing exploded NMR machine that doesn't even belong to Birkbeck.
"When [other student] did the mass spec on his product, it didn't have the right molecular weight. I eventually realised it was because the methanol and water present were forming a hemiacetal."
"And... what was the problem?".
"Well, just that it took me so long to work out what was wrong."
"Did [other student] throw his product away, thinking he'd made the wrong thing?"
"No, he's still got it."

Get this. I am working for a man whose idea of a disaster is getting the wrong molecular weight on a mass spectrum. What the hell does he call it when there's a massive explosion and you're removing shards of glass from your skin and scraping product off the ceiling?

I'm doomed, aren't I?

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