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Genome, see what you are doing
As I've been unable to connect to seti@home for so long I thought I'd jump in and get the genome@home client up and running. Taking a look in the genome directory I saw the work units actually come in the form of standard pdb files so I thought I'd dig out a couple of programs I use at work to take a look.
You can look at the proteins you are working on by using one of the programs I mention below, the files of interest are input.pdb and output.pdb. Input.pdb is your work unit and contains the protein sequence you are going to be working on. Output.pdb will eventually contain several sequences, these are the 30 or whatever you generate when you crunch a WU, once you have finished one its sequence gets written out.
I presume when you load the output.pdb into Rasmol for example you are just looking at the first listed sequence and you can look at the others by copying them out to seperate pdb files, just load a copy of output.pdb into a text editor and chop out a sequence that lies between
MODEL 1
ATOM 1 N ILE 1 -3.376 31.880 17.428
ATOM 2 CA ILE 1 -3.013 30.524 16.989
...
...
ATOM 937 CG PRO 91 18.752 20.215 0.886
ATOM 938 CD PRO 91 17.470 20.400 1.692
TER
ENDMDL
The number of atoms you have will vary depending on the protein you are working on. Then just save it as a text file and give it a .pdb extension. As I say work on a copy and don't overwrite the original file!
<a href="http://www.murc.ws/Utils/rasmol2.exe">Rasmol For Windows (193KB)</a> is a nice little viewer, you can load up the sequence, choise various viewing methods, ball and stick, space filling etc, and freely rotate it. Rasmol has since evolved into the Chime viewer I think it is that comes as a browser extension, I prefer Rasmol.
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<a href="http://www.murc.ws/Utils/vmd16.exe">VMD (3.5MB)</a> is similar to Rasmol but more advanced and uses OpenGL for prettier graphics. The other good thing is you can output from VMD into povray description files which you can then load up into <a href="http://www.murc.ws/Utils/povwin3.exe">Povray for Windows (5MB)</a> and render out. Below is an image I did for a report at work, it's a mutant of Firefly Luciferase, Photinus pyralis, that I've been working with.
<center>
You can look at the proteins you are working on by using one of the programs I mention below, the files of interest are input.pdb and output.pdb. Input.pdb is your work unit and contains the protein sequence you are going to be working on. Output.pdb will eventually contain several sequences, these are the 30 or whatever you generate when you crunch a WU, once you have finished one its sequence gets written out.
I presume when you load the output.pdb into Rasmol for example you are just looking at the first listed sequence and you can look at the others by copying them out to seperate pdb files, just load a copy of output.pdb into a text editor and chop out a sequence that lies between
MODEL 1
ATOM 1 N ILE 1 -3.376 31.880 17.428
ATOM 2 CA ILE 1 -3.013 30.524 16.989
...
...
ATOM 937 CG PRO 91 18.752 20.215 0.886
ATOM 938 CD PRO 91 17.470 20.400 1.692
TER
ENDMDL
The number of atoms you have will vary depending on the protein you are working on. Then just save it as a text file and give it a .pdb extension. As I say work on a copy and don't overwrite the original file!
<a href="http://www.murc.ws/Utils/rasmol2.exe">Rasmol For Windows (193KB)</a> is a nice little viewer, you can load up the sequence, choise various viewing methods, ball and stick, space filling etc, and freely rotate it. Rasmol has since evolved into the Chime viewer I think it is that comes as a browser extension, I prefer Rasmol.
<center>
</center>
<a href="http://www.murc.ws/Utils/vmd16.exe">VMD (3.5MB)</a> is similar to Rasmol but more advanced and uses OpenGL for prettier graphics. The other good thing is you can output from VMD into povray description files which you can then load up into <a href="http://www.murc.ws/Utils/povwin3.exe">Povray for Windows (5MB)</a> and render out. Below is an image I did for a report at work, it's a mutant of Firefly Luciferase, Photinus pyralis, that I've been working with.
<center>
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