Opening a Large Number of PDB’s a few at a Time

I sometimes find it convenient to open a large number of pdb files for visualization a few at a time (to check alignment, bond orders…). And I had originally had a bit of trouble coming up with an easy way to do this. I imagine this is somewhat ubuntu/gnome specific, but I thought it might be helpful to some folk:

ls *.pdb|xargs -n 10 gnome-terminal –disable-factory -x /opt/bin/vmd -nt -m

The Important Bit of the PDB File Format

So I find that I occasionally have to look up the pdb_format so I’ve just posted it here (pdf format).  Note that this is only the ATOM line format, but that’s generally what I’m interested in.  Hope this is convenient to at least one other person.

Also see here:

COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
1 -  6        Record name   "ATOM  "
7 - 11        Integer       serial       Atom  serial number.
13 - 16        Atom          name         Atom name.
17             Character     altLoc       Alternate location indicator.
18 - 20        Residue name  resName      Residue name.
22             Character     chainID      Chain identifier.
23 - 26        Integer       resSeq       Residue sequence number.
27             AChar         iCode        Code for insertion of residues.
31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
55 - 60        Real(6.2)     occupancy    Occupancy.
61 - 66        Real(6.2)     tempFactor   Temperature  factor.
77 - 78        LString(2)    element      Element symbol, right-justified.
79 - 80        LString(2)    charge       Charge  on the atom.

Success

Or at least a little bit. I’ve got one machine folding what seems pretty consistently now. Unfortunately can’t post a link to a live image from extreme overclockers, who have a great stats site, far better than stanford’s in my opinion. So stop by and check them out. I’m on teamUbuntu, which seems appropriate to me. And in possibly one of the more interesting stats, active folders, we’re in 27th place. In actual rank we’re currently 75th, and doing pretty well it seems, set to move up 4 slots in the next 2 months. Maybe a tiny bit quicker because of my contribution.

folding at home at extreme overclocking

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Folding at Home

So I’ve recently been trying to set up folding at home. Actually on two different machines and I haven’t been terribly successful. The first machine is a very fast quad core machine living at my parent’s house. I had previously overclocked the q9550 to 3.7 or so GHz. I ended up getting some computation errors, which I believe are due to the degree of the overclock. I don’t have physical access to the machine so I have to wait a bit before someone can back it off for me. The second machine is a machine at my office, and I have actually been having troubles getting it to successfully connect to the collection server to turn in completed work units. I have attempted to set up a proxy and hopefully that solves that problem. But I still haven’t seen if it will work.

System 1: q9550 @ 3.655 GHz, problem is mistakes in computation, plan is to slow down the clock speed by 5% or so to 3.485 GHz, and I’ll see how that settles it.
System 2: E7200 @ 2.53GHz, problem is firewall, we’ll see if the proxy helps matters any

I would love to try building a machine that could collect more than 10k ppd. After looking into the issue a bit it appears that an i7 based machine is only marginally more expensive than a core2quad based machine. So I would of course be leaning that way. Though I think I could give the components some time to decrease in price. Also it seems the sweet spot for a gpu folding is the $100 mark. Of course the $500 cards could fold better, but I’d never consider spending that much on just folding, since I’m not much of a gamer. The plan would be an i7 and then two 9800 GT cards, aiming to balance the somewhat competing goals of cost, speed (points per day), and energy consumption.

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