[gmx-users] Ramachandran Plot for a Polymer
Dear Gromacs Users, Can we get the Ramachandran plot for a polymer using Gromacs? If we can, how do we do that? Appreciate your help. Thank you. -- Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
> Message: 4 > Date: Wed, 9 Jan 2019 11:59:31 +0100 > From: Tamas Hegedus > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] ramachandran plot > Message-ID: <563a0c65-532e-a47d-fdf7-5046a062c...@hegelab.org> > Content-Type: text/plain; charset=utf-8; format=flowed Hi Tamas Thank you so much for your suggestion. I will check that. Just to know one more thing, is there any program to know only number of residues in the allowed and favoured region in the output? Thank You > Hi, > > I use the python MDAnalysis packages for this. > > https://github.com/MDAnalysis/mdanalysis/issues/1335 > > https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html > > Have a nice day, Tamas > > On 01/09/2019 10:30 AM, za...@tezu.ernet.in wrote: >> Dear Users >> >> Can anyone suggest me any available tool to analyze ramachandran plot >> timewise for a trajectory? >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> India >> >> >> >> >> >> >> >> * * * D I S C L A I M E R * * * >> This e-mail may contain privileged information and is intended solely >> for the individual named. If you are not the named addressee you should >> not disseminate, distribute or copy this e-mail. Please notify the >> sender immediately by e-mail if you have received this e-mail in error >> and destroy it from your system. Though considerable effort has been >> made to deliver error free e-mail messages but it can not be guaranteed >> to be secure or error-free as information could be intercepted, >> corrupted, lost, destroyed, delayed, or may contain viruses. The >> recipient must verify the integrity of this e-mail message. >> > > > -- > Tamas Hegedus, PhD > Senior Research Fellow > Department of Biophysics and Radiation Biology > Semmelweis University | phone: (36) 1-459 1500/60233 > Tuzolto utca 37-47| mailto:ta...@hegelab.org > Budapest, 1094, Hungary | http://www.hegelab.org > > > -- Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
> Message: 5 > Date: Wed, 9 Jan 2019 17:17:31 +0530 > From: Subhomoi Borkotoky > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] ramachandran plot > Message-ID: > > Content-Type: text/plain; charset="UTF-8" Hii Subhomoi Thank you so much for your suggestion. Regards Zaved > Hi Javed, > > I hope *gmx rama* will solve the issue. > > http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html > > > Thanks & Regards, > -- > *Subhomoi Borkotoky, Ph. D.* > DBT Research Associate, > Kusuma School of Biological Sciences, > Indian Institute of Technology Delhi, > New Delhi-110016, > India. > > Alternate E-mail : subho...@yahoo.com > > > > > > On Wed, Jan 9, 2019 at 3:01 PM wrote: > >> Dear Users >> >> Can anyone suggest me any available tool to analyze ramachandran plot >> timewise for a trajectory? >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
Hi Javed, I hope *gmx rama* will solve the issue. http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* DBT Research Associate, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India. Alternate E-mail : subho...@yahoo.com On Wed, Jan 9, 2019 at 3:01 PM wrote: > Dear Users > > Can anyone suggest me any available tool to analyze ramachandran plot > timewise for a trajectory? > > Thank You > > Regards > Zaved Hazarika > Research Scholar > Dept. Of Molecular Biology and Biotechnology, > Tezpur University, > India > > > > > > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
Hi, I use the python MDAnalysis packages for this. https://github.com/MDAnalysis/mdanalysis/issues/1335 https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html Have a nice day, Tamas On 01/09/2019 10:30 AM, za...@tezu.ernet.in wrote: Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta...@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ramachandran plot
Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Thank you Dear Mark. Its my pleasure taking your time. ;-) On Wed, Jun 7, 2017 at 2:25 PM, Mark Abraham wrote: > Hi, > > This is why you should actually copy and paste your command lines so you > don't waste your time ;-) And mine. > > Unless you wrote your entire system to your xtc file, your tpr has more > atoms than your xtc, and thus probably some more dihedrals. Make a matching > subset of your tpr using gmx convert-tpr, and use that with gmx rama -s. > > Mark > > On Wed, Jun 7, 2017 at 10:41 AM RAHUL SURESH > wrote: > > > Dear Mark > > Thank you > > > > gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg > > > > This was my command.. > > > > I didn't choose any dihedral particularly > > > > > > On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > Sounds like your choice of dihedrals doesn't match your system. How did > > you > > > select them? > > > > > > Mark > > > > > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > > > > > > > Dear Users > > > > > > > > When I try to execute ramachandran plot analysis, I get the following > > > note > > > > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > > > > (nearly 30-40 dihedrals). What is it about? > > > > > > > > Input is just protein structure extended upto 150ns. > > > > > > > > -- > > > > *Regards,* > > > > *Rahul Suresh* > > > > *Research Scholar* > > > > *Bharathiar University* > > > > *Coimbatore* > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Hi, This is why you should actually copy and paste your command lines so you don't waste your time ;-) And mine. Unless you wrote your entire system to your xtc file, your tpr has more atoms than your xtc, and thus probably some more dihedrals. Make a matching subset of your tpr using gmx convert-tpr, and use that with gmx rama -s. Mark On Wed, Jun 7, 2017 at 10:41 AM RAHUL SURESH wrote: > Dear Mark > Thank you > > gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg > > This was my command.. > > I didn't choose any dihedral particularly > > > On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham > wrote: > > > Hi, > > > > Sounds like your choice of dihedrals doesn't match your system. How did > you > > select them? > > > > Mark > > > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > > > > > Dear Users > > > > > > When I try to execute ramachandran plot analysis, I get the following > > note > > > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > > > (nearly 30-40 dihedrals). What is it about? > > > > > > Input is just protein structure extended upto 150ns. > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Dear Mark Thank you gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg This was my command.. I didn't choose any dihedral particularly On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham wrote: > Hi, > > Sounds like your choice of dihedrals doesn't match your system. How did you > select them? > > Mark > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > > > Dear Users > > > > When I try to execute ramachandran plot analysis, I get the following > note > > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > > (nearly 30-40 dihedrals). What is it about? > > > > Input is just protein structure extended upto 150ns. > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Hi, Sounds like your choice of dihedrals doesn't match your system. How did you select them? Mark On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > Dear Users > > When I try to execute ramachandran plot analysis, I get the following note > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > (nearly 30-40 dihedrals). What is it about? > > Input is just protein structure extended upto 150ns. > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Ramachandran plot
Dear Users When I try to execute ramachandran plot analysis, I get the following note like "Dihedral around 5809,5816 not found in topology. Using mult=3" (nearly 30-40 dihedrals). What is it about? Input is just protein structure extended upto 150ns. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
Hi Tsjerk,
I was wondering how did you get the input.dat file? did you got it from
grace/xmgrace? I was able to save the plot in .ps or .png format file.
However whenever I tried to run kde2d.r I was getting an error:
Please see below:
./kde2d.r ramachandran.png ramachandran-2.png
./kde2d.r: line 11: syntax error near unexpected token `('
./kde2d.r: line 11: `args <- commandArgs()'
what could be wrong?
best regards
Urszula
> Hi Urszula,
>
> Save the following as kde2d.r and make it executable. Then you can run
>
> ./kde2d.r rama.dat rama.png
>
> Cheers,
>
> Tsjerk
>
> kde2d.r
>
> #!/usr/bin/env Rscript
>
> # Script for drawing 2D combined linear/circular KDE plots.
> #
> # (c)2014 Tsjerk A. Wassenaar
> # Friedrich-Alexander University of Erlangen-Nuremberg
>
>
> args <- commandArgs()
> args <- args[-(1:match("--args", args))]
>
>
> # MASS library is needed for bandwidths
> require(MASS)
>
>
> # This 2D circular KDE function was developed for correct handling
> # of bivariate angular data as part of the orientational analysis
> # used with DAFT (Manuscript submitted).
> kde2d <- function (x, y, h, n = 25, xlim, ylim, circular=TRUE, phase=0)
> {
> if (length(y) != length(x))
> stop("data vectors must be the same length")
>
> n<- rep(n, length.out = 2L)
> phase<- rep(phase, length.out = 2L)
> circular <- rep(circular, length.out = 2L)
>
> s <- which(!is.na(x) | !is.na(y))
> x <- x[s]
> y <- y[s]
>
> nx <- length(x)
>
> if (any(!is.finite(x)) || any(!is.finite(y)))
> stop("missing or infinite values in the data are not allowed")
>
>
> if (circular[1])
> x <- (x+180)%%360-180
>
> if (circular[2])
> y <- (y+180)%%360-180
>
>
> if (missing(xlim))
> xlim <- if (circular[1]) c(-180,180) else range(x)
>
> if (missing(ylim))
> ylim <- if (circular[2]) c(-180,180) else range(y)
>
> if (any(!is.finite(c(xlim,ylim
> stop("only finite values are allowed in 'xlim' and 'ylim'")
>
>
> h <- if (missing(h))
> c(bandwidth.nrd(x), bandwidth.nrd(y))
> else rep(h, length.out = 2L)
> if (any(h <= 0))
> stop("bandwidths must be strictly positive")
> h <- h/4
>
>
> if (circular[1])
> {
> gx <- seq.int(-180, 180, length.out = n[1L])
> ax <- ((outer(gx, x-phase[1], "-")+180)%%360-180)/h[1L]
> gx <- gx + phase[1]
> }
> else
> {
> gx <- seq.int(xlim[1], xlim[2], length.out = n[1L])
> ax <- outer(gx, x, "-")/h[1L]
> }
>
>
> if (circular[2])
> {
> gy <- seq.int(-180, 180, length.out = n[2L])
> ay <- ((outer(gy, y-phase[2], "-")+180)%%360-180)/h[2L]
> gy <- gy + phase[2]
> }
> else
> {
> gy <- seq.int(ylim[1], ylim[2], length.out = n[2L])
> ay <- outer(gy, y, "-")/h[2L]
> }
>
>
> z <- tcrossprod(matrix(dnorm(ax), , nx), matrix(dnorm(ay), , nx))/(nx
> *
> h[1L] * h[2L])
>
>
> list(x = gx, y = gy, z = z)
> }
>
>
> # Color gradients for coloring density plots
>
> rng <- seq(0,1,length.out=100)
>
> white2red <- rgb(1,rev(rng),rev(rng))
> blue2white<- rgb(rng,rng,1)
>
> # Rainbow
> magenta2red <- rgb(1,0,rev(rng))
> red2yellow<- rgb(1,rng,0)
> yellow2green <- rgb(rev(rng),1,0)
> green2cyan<- rgb(0,1,rng)
> cyan2blue <- rgb(0,rev(rng),1)
>
> red2orange<- rgb(1,0.5*rng,0)
> orange2yellow <- rgb(1,0.5+0.5*rng,0)
>
>
>
> data <- read.table(args[1])
> d<- kde2d(data[,1],data[,2])
>
>
> ## Plotting density images
>
> # Here the density images are prepared and written to file. The first one
> (WT) is explained in detail:
>
> #---Start of image---
>
> # Wildtype
>
> # Start a 1200x1200 png file, with a font size (for labels) of 40 points
> # Changing the resolution requires changing the font size to keep the
> relative size.
> png(
> args[2],
> width=1200,
> height=1200,
> pointsize=40
> )
>
> # Write an image of the density for WT
> image(
> d$x, d$y, d$z, # Image data X/Y and intensity (Z)
> zlim=c(0,max(d$z)),# Limits for coloring
> xlab=expression(phi), # X-label text. expression(beta) gives the
> greek
> character
> ylab=expression(psi), # Y-label text.
> main="", # Main title. Can be set to "" to suppress
> title.
> bty="n", # Surrounding box type. To draw a thicker box,
> the box is here suppressed, using "n" for None.
> col=c(white2red,red2orange,orange2yellow)
> )
>
> box(lwd=3) # Add a box with a thicker line. Change this to
> match the resolution of the imge.
> # Add points
> points(data[,1], data[,2], pch=".", cex=1)
>
> # Add contour lines
> contour(
> d$x, d$y, d$z,
> zlim=c(0,max(d$z)),
> add=TRUE, # If add=FALSE (default), then 'contour' starts
> a new plot.
> labels="", # Suppress labels on contour lines
> labcex=0.001, # To avoid
Re: [gmx-users] ramachandran plot
Hi Urszula,
Save the following as kde2d.r and make it executable. Then you can run
./kde2d.r rama.dat rama.png
Cheers,
Tsjerk
kde2d.r
#!/usr/bin/env Rscript
# Script for drawing 2D combined linear/circular KDE plots.
#
# (c)2014 Tsjerk A. Wassenaar
# Friedrich-Alexander University of Erlangen-Nuremberg
args <- commandArgs()
args <- args[-(1:match("--args", args))]
# MASS library is needed for bandwidths
require(MASS)
# This 2D circular KDE function was developed for correct handling
# of bivariate angular data as part of the orientational analysis
# used with DAFT (Manuscript submitted).
kde2d <- function (x, y, h, n = 25, xlim, ylim, circular=TRUE, phase=0)
{
if (length(y) != length(x))
stop("data vectors must be the same length")
n<- rep(n, length.out = 2L)
phase<- rep(phase, length.out = 2L)
circular <- rep(circular, length.out = 2L)
s <- which(!is.na(x) | !is.na(y))
x <- x[s]
y <- y[s]
nx <- length(x)
if (any(!is.finite(x)) || any(!is.finite(y)))
stop("missing or infinite values in the data are not allowed")
if (circular[1])
x <- (x+180)%%360-180
if (circular[2])
y <- (y+180)%%360-180
if (missing(xlim))
xlim <- if (circular[1]) c(-180,180) else range(x)
if (missing(ylim))
ylim <- if (circular[2]) c(-180,180) else range(y)
if (any(!is.finite(c(xlim,ylim
stop("only finite values are allowed in 'xlim' and 'ylim'")
h <- if (missing(h))
c(bandwidth.nrd(x), bandwidth.nrd(y))
else rep(h, length.out = 2L)
if (any(h <= 0))
stop("bandwidths must be strictly positive")
h <- h/4
if (circular[1])
{
gx <- seq.int(-180, 180, length.out = n[1L])
ax <- ((outer(gx, x-phase[1], "-")+180)%%360-180)/h[1L]
gx <- gx + phase[1]
}
else
{
gx <- seq.int(xlim[1], xlim[2], length.out = n[1L])
ax <- outer(gx, x, "-")/h[1L]
}
if (circular[2])
{
gy <- seq.int(-180, 180, length.out = n[2L])
ay <- ((outer(gy, y-phase[2], "-")+180)%%360-180)/h[2L]
gy <- gy + phase[2]
}
else
{
gy <- seq.int(ylim[1], ylim[2], length.out = n[2L])
ay <- outer(gy, y, "-")/h[2L]
}
z <- tcrossprod(matrix(dnorm(ax), , nx), matrix(dnorm(ay), , nx))/(nx *
h[1L] * h[2L])
list(x = gx, y = gy, z = z)
}
# Color gradients for coloring density plots
rng <- seq(0,1,length.out=100)
white2red <- rgb(1,rev(rng),rev(rng))
blue2white<- rgb(rng,rng,1)
# Rainbow
magenta2red <- rgb(1,0,rev(rng))
red2yellow<- rgb(1,rng,0)
yellow2green <- rgb(rev(rng),1,0)
green2cyan<- rgb(0,1,rng)
cyan2blue <- rgb(0,rev(rng),1)
red2orange<- rgb(1,0.5*rng,0)
orange2yellow <- rgb(1,0.5+0.5*rng,0)
data <- read.table(args[1])
d<- kde2d(data[,1],data[,2])
## Plotting density images
# Here the density images are prepared and written to file. The first one
(WT) is explained in detail:
#---Start of image---
# Wildtype
# Start a 1200x1200 png file, with a font size (for labels) of 40 points
# Changing the resolution requires changing the font size to keep the
relative size.
png(
args[2],
width=1200,
height=1200,
pointsize=40
)
# Write an image of the density for WT
image(
d$x, d$y, d$z, # Image data X/Y and intensity (Z)
zlim=c(0,max(d$z)),# Limits for coloring
xlab=expression(phi), # X-label text. expression(beta) gives the greek
character
ylab=expression(psi), # Y-label text.
main="", # Main title. Can be set to "" to suppress title.
bty="n", # Surrounding box type. To draw a thicker box,
the box is here suppressed, using "n" for None.
col=c(white2red,red2orange,orange2yellow)
)
box(lwd=3) # Add a box with a thicker line. Change this to
match the resolution of the imge.
# Add points
points(data[,1], data[,2], pch=".", cex=1)
# Add contour lines
contour(
d$x, d$y, d$z,
zlim=c(0,max(d$z)),
add=TRUE, # If add=FALSE (default), then 'contour' starts
a new plot.
labels="", # Suppress labels on contour lines
labcex=0.001, # To avoid gaps in the controu lines (because of
the empty label), set the label size very small
nlevels=20,# Number of lines to draw, between range of
'zlim'
lwd=3 # Width of contour lines. Set to 3 to match png
resolution. Change when changing the resolution.
)
# Close the image file, saving it.
dev.off()
#---End of image---
On Mon, Nov 17, 2014 at 1:44 PM, Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:
> Dear Tsjerk,
>
> Could you send me the script again? as I did not find the attachment in
> your previous email.
>
> best regards
> Urszula
>
>
> > Hi Urszula,
> >
> > Attached is an R script for drawing 2D circular or combined
> > circular/linear
> > KDEs. It works as a comm
Re: [gmx-users] ramachandran plot
Dear Tsjerk,
Could you send me the script again? as I did not find the attachment in
your previous email.
best regards
Urszula
> Hi Urszula,
>
> Attached is an R script for drawing 2D circular or combined
> circular/linear
> KDEs. It works as a command line script, taking as arguments a file with
> 2-column data, and an output image file name (./kde2d.r input.dat
> output.png). It's pretty easy to adapt to suit your needs, even if you
> don't know R specifically. I wrote the routine for a manuscript we just
> submitted, where the method is explained in some detail, and if you like
> the images and care to use it for publications, I would be obliged if you
> could reference that paper ("High-Throughput Simulations of Dimer and
> Trimer Assembly of Membrane Proteins. The DAFT approach."). If you run
> into
> problems or have further questions, please let me know.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Nov 14, 2014 at 4:31 PM, Urszula Uciechowska <
> urszula.uciechow...@biotech.ug.edu.pl> wrote:
>
>> Could you please send me the code? It can be on my private email.
>>
>> Thanks a lot
>>
>> Ursuzla
>>
>> > Hi Urszula,
>> >
>> > It's a while ago that I made that one, and I don't have the code at
>> hand.
>> > But it's a combination of a density plot (kde2d) with the points laid
>> > over,
>> > and a polygon to highlight the forbidden region. These days I'm doing
>> > circular 2D KDEs, whic is more correct. I can send the R code for thay
>> if
>> > you want.
>> >
>> > Best,
>> >
>> > Tsjerk
>> > On Nov 14, 2014 12:34 PM, "Urszula Uciechowska" <
>> > urszula.uciechow...@biotech.ug.edu.pl> wrote:
>> >
>> >> Dear Gromacs users,
>> >>
>> >> I generated the ramachandran plot and would like to colour it in
>> xmgrace
>> >> as it was shown in tutorial:
>> >> http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
>> >>
>> >> Does anyone know how to do it?
>> >>
>> >> Best regards
>> >> Urszula Uciechowska
>> >>
>> >>
>> >>
>> >>
>> >> -
>> >> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>> >> http://www.ug.edu.pl/
>> >>
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-requ...@gromacs.org.
>> >>
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send
>> > a mail to gmx-users-requ...@gromacs.org.
>> >
>>
>>
>> University of Gdansk and Medical Univesity of Gdansk
>> Department of Molecular and Cellular Biology
>> ul. Kladki 24
>> 80-822 Gdansk
>> Poland
>>
>>
>> -
>> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>> http://www.ug.edu.pl/
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-requ...@gromacs.org.
>
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland
-
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
Hi Urszula,
Attached is an R script for drawing 2D circular or combined circular/linear
KDEs. It works as a command line script, taking as arguments a file with
2-column data, and an output image file name (./kde2d.r input.dat
output.png). It's pretty easy to adapt to suit your needs, even if you
don't know R specifically. I wrote the routine for a manuscript we just
submitted, where the method is explained in some detail, and if you like
the images and care to use it for publications, I would be obliged if you
could reference that paper ("High-Throughput Simulations of Dimer and
Trimer Assembly of Membrane Proteins. The DAFT approach."). If you run into
problems or have further questions, please let me know.
Cheers,
Tsjerk
On Fri, Nov 14, 2014 at 4:31 PM, Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:
> Could you please send me the code? It can be on my private email.
>
> Thanks a lot
>
> Ursuzla
>
> > Hi Urszula,
> >
> > It's a while ago that I made that one, and I don't have the code at hand.
> > But it's a combination of a density plot (kde2d) with the points laid
> > over,
> > and a polygon to highlight the forbidden region. These days I'm doing
> > circular 2D KDEs, whic is more correct. I can send the R code for thay if
> > you want.
> >
> > Best,
> >
> > Tsjerk
> > On Nov 14, 2014 12:34 PM, "Urszula Uciechowska" <
> > urszula.uciechow...@biotech.ug.edu.pl> wrote:
> >
> >> Dear Gromacs users,
> >>
> >> I generated the ramachandran plot and would like to colour it in xmgrace
> >> as it was shown in tutorial:
> >> http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
> >>
> >> Does anyone know how to do it?
> >>
> >> Best regards
> >> Urszula Uciechowska
> >>
> >>
> >>
> >>
> >> -
> >> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> >> http://www.ug.edu.pl/
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send
> > a mail to gmx-users-requ...@gromacs.org.
> >
>
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Tsjerk A. Wassenaar, Ph.D.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
Could you please send me the code? It can be on my private email. Thanks a lot Ursuzla > Hi Urszula, > > It's a while ago that I made that one, and I don't have the code at hand. > But it's a combination of a density plot (kde2d) with the points laid > over, > and a polygon to highlight the forbidden region. These days I'm doing > circular 2D KDEs, whic is more correct. I can send the R code for thay if > you want. > > Best, > > Tsjerk > On Nov 14, 2014 12:34 PM, "Urszula Uciechowska" < > urszula.uciechow...@biotech.ug.edu.pl> wrote: > >> Dear Gromacs users, >> >> I generated the ramachandran plot and would like to colour it in xmgrace >> as it was shown in tutorial: >> http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html >> >> Does anyone know how to do it? >> >> Best regards >> Urszula Uciechowska >> >> >> >> >> - >> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego >> http://www.ug.edu.pl/ >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
Hi Urszula, It's a while ago that I made that one, and I don't have the code at hand. But it's a combination of a density plot (kde2d) with the points laid over, and a polygon to highlight the forbidden region. These days I'm doing circular 2D KDEs, whic is more correct. I can send the R code for thay if you want. Best, Tsjerk On Nov 14, 2014 12:34 PM, "Urszula Uciechowska" < urszula.uciechow...@biotech.ug.edu.pl> wrote: > Dear Gromacs users, > > I generated the ramachandran plot and would like to colour it in xmgrace > as it was shown in tutorial: > http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html > > Does anyone know how to do it? > > Best regards > Urszula Uciechowska > > > > > - > Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego > http://www.ug.edu.pl/ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ramachandran plot
Dear Gromacs users, I generated the ramachandran plot and would like to colour it in xmgrace as it was shown in tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Does anyone know how to do it? Best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
