It really depend on what you want to show your reader.
But in generally, I would think about
histogram
<
https://www.researchgate.net/profile/Bjoern_Braunschweig/publication/278026357/figure/fig10/AS:294365093220355@1447193515130/Figure-S11-Histogram-of-Dihedral-angles-within-15-A-of-the-center-of-interaction-Insert.png>
ramachandran plot
<
http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/ramachandran/other/rampage_1hmp.png>
pandas' Dataframe in Jupyter notebook
<
https://www.google.com/search?q=dihedral+histogram&rlz=1C1CHMO_enUS485US485&espv=2&biw=1745&bih=883&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiavLze8rrNAhWKND4KHbFCBu8Q_AUIBigB#tbm=isch&q=pandas+dataframe&imgrc=_>
PS: Please do not quote other replies from other topics. It's really
confusing.
Hai
On Wed, Jun 22, 2016 at 1:17 AM, Sehrish Naz Aijaz <sehrish.naz.outlook.com>
wrote:
> Dear All,
> I have run protein-protein simulation to investigate the conformational
> changes in protein after binding with its ligand protein. I have plotted
> the graphs of dihedral angles using Cpptraj tool in amber. Though I can
> present my results in the graphical form but the number of graphs would be
> needed for that which will exhaust the reader. Therefore, I want to know is
> there a better tool to present the cumulative data on dihedral angles in
> either a tabulated or graphical form.
>
> Regards,
>
> Sehrish Naz
>
> Jr. Research Fellow,
> Computational Chemistry Unit.
> Dr. Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75270.
> E-mail: Sehrish.naz.outlook.com
>
> From: David A Case<mailto:david.case.rutgers.edu>
> Sent: 21 June 2016 22:25
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] Problem analysing output with process_mdout.perl
> script
>
> On Tue, Jun 21, 2016, Ruth Helena Tichauer wrote:
> >
> > When analysing my output files with the script “process_mdout.perl”, I
> > find that it is not retrieving the density, nor the volume, of my system
> > as both summary.DENSITY and summary.VOLUME files only contain the time
> > elapsed. Am I using an “old” version? You can find it in attachements.
>
> First, try process_mdout.perl on a sample mdout file like this one:
> $AMBERHOME/test/ubiquitin/mdout.ubiquitin.save.
>
> Second, as a sanity check, make sure you actually have Density and VOLUME
> lines in your mdout file.
>
> ...good luck...dac
>
>
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Received on Tue Jun 21 2016 - 23:00:02 PDT
