[Fwd: Cannot generate the plot of DOPE?]
-------- Original Message -------- Subject: Cannot generate the plot of DOPE? Date: Wed, 9 May 2007 02:03:18 +0900 From: Ngo Duc Tri ngoductri@gmail.com To: modeller-care@salilab.org
Dear Modeller users, I finished modelling my protein and doing the evaluation step. I run the file evaluate_model.py to calculate the DOPE score of my model. I got DOPE score : -39521.605469 and there was no error in the log file.
I use this profile file to generate the DOPE plot using GNUPLOT but this program show a strange line. Actually It just show the position of my aminoacid but no DOPE score for each.
I run the GNUPLOT and used the command: plot ' myprotein.profile'
I want to ask you If it's the error of GNUPLOT or my profile file? And how can i fix it to show the actual DOPE score for each residues.
Thank you very much for your comments, Best regards, TriNgo Sungkyunkwan University
> I finished modelling my protein and doing the evaluation step. I run the > file evaluate_model.py to calculate the DOPE score of my model. > I got DOPE score : -39521.605469 and there was no error in the log file. > > I use this profile file to generate the DOPE plot using GNUPLOT but this > program show a strange line. Actually It just show the position of my > aminoacid but no DOPE score for each.
That's because gnuplot by default will plot the first column on your y axis, and the first column in the profile file is just the residue number, so it'll plot [1,1], [2,2], [3,3] etc. - i.e. a line. You need to plot the last column (column 42) which is the total energy. In gnuplot you can do this with a command like
plot "myprotein.profile" using 1:42 with lines
Ben Webb, Modeller Caretaker
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Modeller Caretaker