pyMOL can bite my...

Figure 1. My favorite protein's active site

No more pyMOL for me. I have now been converted to the wonders and joys of using VMD. Not only is it free but the user-friendlyness of this program is astounding. It, to my knowledge, has the same sort of capabilities as pyMOL (i.e. alignments, distance determination, etc.) and can still be used with python (if you are so inclined).

If you are like me and are not a hardcore crystallographer but still want to be able to quickly generate awesome looking structure figures from pdb files or just want to see the relative positioning of residues in protein active sites, then VMD is amazing...

I have arrived?

Its quite out here. I am sitting on my screen porch, the only light is from the glowing laptop screen. The hubby is in bed and the kitty has resumed her post as the guard of the night on the beat-up file cabinet placed next to the windows. It, I think, has finally hit that I "made it." That I got through all the bullshit from grad school, that I somehow survived and came out stronger, tougher and smarter- OK, maybe not smarter, but you know what I mean.

Then I realize that that yeah, I made it through grad school, but now I have to make it through the post-doc (much much much more enjoyable for several reasons), then make it through the job hunt, then make it through tenure or promotions or whatever the hell else I plan on doing. Right now, though everything is wide open.

But when is it done? When can you finally sit back, sigh, and say "I have arrived"? Is there one culminating moment that defines the hours at the bench, the days in the library, the years tapping away at the keyboard searching and hunting for that one elusive idea, the one hair-brained experiment, the onepiece of data that not only finishes the story but tells it far better than anyone else has? When, as the average scientist who loves toiling away at the bench, who does basic research on, some would say, not so hot and sexy systems, but who slowly lays the foundation for others to jump off and run with the newest buzz-word laden research, can I say I have finally arrived?

Not yet and maybe not ever for me, because in my humble opinion, thinking I have arrived means that I have reached my ultimate potential- and I don't want to think about that. I want to think that I can keep getting better, keep learning, keep growing as a scientist and researcher. I can never fully understand everything, but I think that I am going to damn-well try.

bad mojo

After a llloooonnnnngg hiatus, I decided to come back and write some more. Actually, it was more due to the fact that the new laptop finally arrived (seriously Dell- an order on May 5th translates to shipment on June 20? Really?) and I don't really like blogging in lab (too many busy bodies mulling around). Did I mention I now am a proud owner of a pink, yes pink, laptop. And not by choice, mind you. I am not exactly a pink type of girl- the hard-rock, tattoos, nose piercing, jeans-and-tennis-shoes personality I exude does not exactly scream "Ohhhh, pink how cute! and bunnies! and flowers! awwww...." But I do have to admit, its metallic pink and somewhat cool looking and Dell did donate 5$ (a whole five dollars!) to the Susan G. Komen fund so its bearable. And fast. And shiny. OK, enough about the laptop.

The last month in the lab has sucked the life out of me. For the past three weeks we have been dealing with two evacuations due to suspected gas leaks (no, they still don't know where its coming from), a three hour power outage (thank god the -80 came back up OK), the IR-MS going down (but is back up again), a lab flood, no air conditioning for a week (mind you- it was 95 degrees outside and 82 degrees in the lab-lord have mercy it was hot), a -20 going down, and for some reasons, three preps of my favorite protein crapped out over night (flocky, fluffy protein== bad bad thing and angry Dr. Zeek).

I finally ran some experiments today and they seemed to work (YAY), the -20 is still chugging along, the IR-MS is now giving reproducible results, the laptop came in and it seems that the humidity has finally moved on from here. Maybe today will be the turning point and I can just chalk May and June up to bad chemistry mojo.

All at once

Everything seems to be happening at once. Emotionally, mentally and physically I am spent.

Galley proofs came in for the paper (did I mention it was accepted with minor revisions...minor as in add two references and a sentence or two)...my first first-author paper (ever) and first paper in new post-doc lab

Fellowship app package arrived safely (or so Fed-Ex says) so now we wait

Offer in on the house we are selling- we accepted and now waiting for the official close date (much more blog ranting fodder on this, but not now)

Preps of MFP and mutated MFP are going but draining...

That's all I have the energy for right now. Things are crazy nuts, but god it feels good to be shaking it up again in the lab. Post more later...

Playing hookey...

Yes, as the last day of spring break winds down across Major Research U, I have decided that in an attempt to keep my sanity and prevent myself from totally loosing my junk in the upcoming days when my undergrad minions come back, I would take today off. Coincidentally, there is an all day long Battlestar Galactica marathon on SciFi today (right now I am watching Gata grow some bals- I never really liked him anyways- Mr DrZeek and I always thought he was a cylon), finishing with the 2 hr series finale, and my fav NCAA basketball team is playing right now (Go...never mind, that may give away too much of my secret identity but its 26-18 at the half- whooo-hooo). I do have my fellowship to work on and some papers to digest before going back to the lab tomorrow (seems backwards, taking off Friday to go in Saturday-but Saturday's are nice, NO ONE, but the PI ever comes in), but I tell you getting up at noon-- something I don't do on the weekends since that's when I and Mr DrZeek run our errands-- drinking some coffee and perusing my fav blogs at my own pace has been refreshing. I think this mental health day is exactly what I needed...

EDIT: oh yeah, went with the hubby to the dentist this morning (woke up at 6:30--got back home at 8:00 and promptly crawled back into bed till noon-anyways, I digress)-they yanked his tooth. Poor babes. At least they gave him some of the "good stuff," too bad he couldn't take off of work (too many deliveries today).

make the writing stop

I just want to get back to some bench work. Seriously. All this writing has put a damper on my mood (and motivation). This silly fellowship is due in two weeks and I have roughly two pages (since that puts me at the limit) to write. Two silly pages. Although, I should mention that I am proposing some crazy science never done with my favorite protein (MFP) that I only have a minimal background on-and of course this is the research design and methods part that I am putting off right now. I even purified some of MFP this week, just* to get my "hands dirty." Former post-doc now PI and I were talking today and he mentioned how this was great training for when/if I get a TT faculty position. Maybe, but I want to still stay in the trenches and just work on some really cool science.

*Not that I didn't/don't always need more of MFP- probably won't touch it for a few weeks, though....

Mission accomplished...

Paper submitted.

Now just waiting for the reviews.

The fact that it is my first first-author paper (my PI in grad school would always put himself as first author) is awesome. The fact that my name is followed by 5 PI's (for a total of 5 universities, none of them within 90 miles of each other- in fact three of them are on different continents) makes me laugh in a sad sort of way.

So, what's on tap for the next 6 months??
Paper 1: submitted
Paper 2: chemicals on back order for very important experiments (VIE), but writing everything else --two months ETA till first round of back and forth corrections
Fellowship Resubmit: due in 20-some odd days. I have opened a word.doc file and named it fellowhipresub.doc, but that is about as far as I am right now
Paper 3: bugs are grown and in the freezer, need to go on a purification spree- ETA of data to send around- 4-5 months (if I put this on the back burner to finish paper 2).

I need to get back to the bench today, if for no other reason than to save my sanity....