<br><br><div class="gmail_quote">On Thu, Nov 5, 2009 at 10:23 AM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
So, what's the advantage over using e.g. (xm)grace?<br></blockquote><div><br>I'm not sure. The last time I tried, xmgrace refused to install on my Mac.<br><br>This certainly isn't a big analysis/plotting package. It's just a quick way to step through XVG files.<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
/Erik<br>
<br>
Michael Lerner skrev:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
Hi,<br>
<br>
(My apologies if this shows up several times. I sent it yesterday, but it appears that it won't go through to the list if I include a screenshot.)<br>
<br>
I wanted a quick way to plot the data in XVG files, so I wrote a quick little GUI viewer in Python this morning. You point it at an XVG file and it pops up a GUI where you can click buttons to step through the columns of data, plot individual columns from the XVG file, or make a plot of everything in the XVG file.<br>
<br>
This makes it easy to dump all the information from an .edr/trr/xtc/etc file and step through it visually in 30 seconds. That, in turn, makes me way more likely to look at as much information as possible as part of my normal workflow.<br>
<br>
I've only tested this on a few of my own XVG files, so it's possible that my simple XVG parser doesn't cover everything.<br>
<br>
Here's the help output. Let me know if anyone finds it useful.<br>
<br>
<br>
Michael-Lerners-MacBook-Pro-2: ~ mglerner$ ./xvgviewer.py --help<br>
Usage: Just a simple XVG viewer.<br>
<br>
For each column in the XVG file, we plot<br>
<br>
- the raw data (light blue)<br>
- a running average (black)<br>
- block averages (green)<br>
<br>
We also print out<br>
<br>
- the average over the simulation<br>
- standard error over the blocks<br>
- average of the standard deviations within each block<br>
<br>
Block length is reported in number of frames, and its meaning will<br>
therefore depend on the settings in your .mdp file as well as the<br>
arguments you used when making the .xvg file.<br>
<br>
We attempt to get units out of the XVG file, and we convert times to<br>
nanoseconds before plotting.<br>
<br>
This program requires<br>
<br>
- Python 2.5 or 2.6<br>
- wxPython 2.8.7.1+ (<a href="http://www.wxpython.org/" target="_blank">http://www.wxpython.org/</a>)<br>
- numpy 1.3.0+ (<a href="http://numpy.scipy.org/" target="_blank">http://numpy.scipy.org/</a>)<br>
- matplotlib 0.99.0+ (<a href="http://matplotlib.sourceforge.net/" target="_blank">http://matplotlib.sourceforge.net/</a>)<br>
- traits 3.2.0+ (<a href="http://code.enthought.com/projects/traits/" target="_blank">http://code.enthought.com/projects/traits/</a>)<br>
<br>
All of which will be installed for you if you use the Enthought Python<br>
Distribution (<a href="http://enthought.com/" target="_blank">http://enthought.com/</a>).<br>
<br>
I mostly wrote this as a quick way to figure out how to use the Traits<br>
GUI, but feel free to email me (m g lerner atsign gmail dot com) if<br>
you have any questions.<br>
<br>
<br>
Options:<br>
-h, --help show this help message and exit<br>
-f FILE, --file=FILE The XVG file [default energy.xvg]<br>
<br>
<br>
Cheers,<br>
<br>
-Michael<br>
<br>
-- <br>
Michael Lerner, Ph.D.<br>
IRTA Postdoctoral Fellow<br>
Laboratory of Computational Biology NIH/NHLBI<br>
5635 Fishers Lane, Room T909, MSC 9314<br>
Rockville, MD 20852 (UPS/FedEx/Reality)<br>
Bethesda MD 20892-9314 (USPS)<br></div></div>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
<br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Laboratory of Molecular Biophysics,<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://xray.bmc.uu.se/molbiophys" target="_blank">http://xray.bmc.uu.se/molbiophys</a><br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br><br clear="all"><br>-- <br>Michael Lerner, Ph.D.<br>IRTA Postdoctoral Fellow<br>Laboratory of Computational Biology NIH/NHLBI<br>5635 Fishers Lane, Room T909, MSC 9314<br>Rockville, MD 20852 (UPS/FedEx/Reality)<br>
Bethesda MD 20892-9314 (USPS)<br>