From: James S. <jms...@gm...> - 2011-11-16 17:50:15
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Dear PyMol Users! I wounder to know about posible ways to plot for my structures different torsion angles (phy, psi, chi ) on the ramachandran map via pymol. In particular I would like to obtain the next information 1- I d like to visualise and measure different torsions for my structure and plot this values on the ramachandran plot 2- I'd like to make such measurements for the enssemble of the pdb structures and plot on the ramachandran map values for each structure ( by points or other markers) Finaly could you show me some tutorials wich could help me working with torsions in pymol? Thanks for your help, James |
From: Thomas H. <sp...@us...> - 2011-11-17 09:39:55
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Hi James, ramachandran plot for the *current* state can be created with the DynoPlot plugin: http://pymolwiki.org/index.php/DynoPlot It uses the API function "get_phipsi", which can calculate phi/psi angles for given states: cmd.get_phipsi(selection='(name ca)', state=-1) Torsion angles other than phi/psi can be calculated with the "get_dihedral" fuction: http://pymolwiki.org/index.php/Get_Dihedral You can also modify torsion angles with "torsion" and "set_dihedral": http://pymolwiki.org/index.php/Set_Dihedral http://pymolwiki.org/index.php/Torsion And you can modify torsion angles interactively using the mouse while in editing mode (pick one atom, then CTRL-Drag). Hope that helps. Cheers, Thomas On 11/16/2011 06:50 PM, James Starlight wrote: > Dear PyMol Users! > > I wounder to know about posible ways to plot for my structures different > torsion angles (phy, psi, chi ) on the ramachandran map via pymol. > > In particular I would like to obtain the next information > > 1- I d like to visualise and measure different torsions for my structure > and plot this values on the ramachandran plot > > 2- I'd like to make such measurements for the enssemble of the pdb > structures and plot on the ramachandran map values for each structure ( > by points or other markers) > > Finaly could you show me some tutorials wich could help me working with > torsions in pymol? > > Thanks for your help, > > James -- Thomas Holder MPI for Developmental Biology |
From: James S. <jms...@gm...> - 2011-11-17 12:27:36
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Hi, Thomas! Thank you for your responce I've tested DynoPlot and have some questions 1- What are the meaning of the symbols in the ramachandran plot ? As I understood the tringle always for the Gly and the square for the Pro. What is the circle ? Could I make some changges that the circle and squire were for any residues in the alpha- helix and betta sheet respectually ? 2- I'm intresting in working with the enssembles of the pdbs' So I 'd like to compare torsions of different residues for different structures in one plot. But when Ive done such comparison I noticed that residues from differen structures were marked on Ramachandran map with the one default colour. How I can specify that residued from different strctures were represented with different colour ? 3- Finally I'd like to compare Chi-1 angle ( rotation on first bond beetween backbone and side chain groups) for my enssemble. How I could mark Chi-1 angle for all my structures and plot in on Rama map? Thanks again, James 2011/11/17 Thomas Holder <sp...@us...> > Hi James, > > ramachandran plot for the *current* state can be created with the DynoPlot > plugin: > http://pymolwiki.org/index.**php/DynoPlot<http://pymolwiki.org/index.php/DynoPlot> > > It uses the API function "get_phipsi", which can calculate phi/psi angles > for given states: > cmd.get_phipsi(selection='(**name ca)', state=-1) > > Torsion angles other than phi/psi can be calculated with the > "get_dihedral" fuction: > http://pymolwiki.org/index.**php/Get_Dihedral<http://pymolwiki.org/index.php/Get_Dihedral> > > You can also modify torsion angles with "torsion" and "set_dihedral": > http://pymolwiki.org/index.**php/Set_Dihedral<http://pymolwiki.org/index.php/Set_Dihedral> > http://pymolwiki.org/index.**php/Torsion<http://pymolwiki.org/index.php/Torsion> > > And you can modify torsion angles interactively using the mouse while in > editing mode (pick one atom, then CTRL-Drag). > > Hope that helps. > > Cheers, > Thomas > > > On 11/16/2011 06:50 PM, James Starlight wrote: > >> Dear PyMol Users! >> >> I wounder to know about posible ways to plot for my structures different >> torsion angles (phy, psi, chi ) on the ramachandran map via pymol. >> >> In particular I would like to obtain the next information >> >> 1- I d like to visualise and measure different torsions for my structure >> and plot this values on the ramachandran plot >> >> 2- I'd like to make such measurements for the enssemble of the pdb >> structures and plot on the ramachandran map values for each structure ( >> by points or other markers) >> >> Finaly could you show me some tutorials wich could help me working with >> torsions in pymol? >> >> Thanks for your help, >> >> James >> > > -- > Thomas Holder > MPI for Developmental Biology > |
From: Thomas H. <sp...@us...> - 2011-11-17 13:20:06
Attachments:
DynoPlot.py
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Hi James, > I've tested DynoPlot and have some questions > > 1- What are the meaning of the symbols in the ramachandran plot ? > As I understood the tringle always for the Gly and the square for the > Pro. What is the circle ? circle is for all other amino acids that are not Gly or Pro. > Could I make some changges that the circle and > squire were for any residues in the alpha- helix and betta sheet > respectually ? sure, it requires little modifications in the script. > 2- I'm intresting in working with the enssembles of the pdbs' So I 'd > like to compare torsions of different residues for different structures > in one plot. But when Ive done such comparison I noticed that residues > from differen structures were marked on Ramachandran map with the one > default colour. How I can specify that residued from different strctures > were represented with different colour ? almost the same modification as for previous question. See attachment for modified script. It colors by atom color and has symbols for secondary structure (sheet=square, helix=triangle). > 3- Finally I'd like to compare Chi-1 angle ( rotation on first bond > beetween backbone and side chain groups) for my enssemble. How I could > mark Chi-1 angle for all my structures and plot in on Rama map? I don't know of any easy solution to that, sorry. Maybe someone else? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology |
From: James S. <jms...@gm...> - 2011-11-17 17:32:01
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Thanks, Thomas It works fine! Could you tell me in what strings the marker for the particular ss element is defined ( e.g I want to change from triangle to oval representation for alpha-helixes )? Thanks Rober I'll try investigate both of that programs, James 2011/11/17 Robert Immormino <imm...@gm...> > James, > > Dangle ( http://kinemage.biochem.duke.edu/software/dangle.php ) from > the Richardson Lab will let you quickly measure a bunch of torsion > angles, and KiNG ( http://kinemage.biochem.duke.edu/software/king.php > ) will let you plot points in up to 7D if I remember correctly. So > you could make a 3D plot of (phi, psi, chi1) of your ensemble with > these two programs. It's been a couple of years, but I could try to > help you navigate this software if you are interested. > > -bob > |
From: Thomas H. <sp...@us...> - 2011-11-17 17:52:33
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Hi James, > Could you tell me in what strings the marker for the particular ss > element is defined ( e.g I want to change from triangle to oval > representation for alpha-helixes )? look for this line: mark = {'H': 'Tri', 'S': 'Rect'}.get(ss, self.mark) I just updated the PyMOLWiki page with the modifications (but markers by secondary structure are disabled by default to not change the previous behaviour). http://pymolwiki.org/index.php/DynoPlot Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2011-11-18 17:39:56
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Dear all :) By the way, I havent tested Dangle software yet but could you tell me any other software wich I could use for torsion angles measurements? As I've mentioned previously I want to calculate different torsions for enssemble of pdb structures and then plot this values on rammachandran plots ( something like I've done via PyMol) Also I'd like to calculate energy difference of the particular structure in accordance to the changing in torsions. What I could use for this purposes besides pymol? Thanks again, James 2011/11/18 Thomas Holder <sp...@us...> > Hi James, > > in principle every python module can be used together with PyMOL! > > With matplotlib I had trouble opening plots on screen because both PyMOL > and matplotlib use Tk. But writing plots to files (png, eps, ...) with > matplotlib should be no problem I guess. > > I again updated http://pymolwiki.org/index.**php/DynoPlot<http://pymolwiki.org/index.php/DynoPlot>to enable postscript export (was quite easy). > > Cheers, > Thomas > > > On 11/18/2011 10:31 AM, James Starlight wrote: > >> Thomas, hello! >> >> In the past I've wrote some scripts in Python biological software but in >> that case I've used matlibplot python module for ploting my graphs. >> Does this module supported by PyMol? >> >> >> James >> >> >> 2011/11/18 Thomas Holder <sp...@us... >> <mailto:speleo3@users.**sourceforge.net <sp...@us...>>> >> >> >> Hi James, >> >> >> by the way how I could save that plots in desired format >> Finally is it possible to make legend on that plot? E.g I want >> indicate >> what marker correspond to what SS and provide my plot with the >> colour >> description ( what colour correspond to what pdb structure ). >> How I could make those things? >> >> >> I guess the easyest way is to take screenshots and add the legend >> with some real drawing tool (like Illustrator, Inkscape, ...). >> >> If you know how to script in python, you may modify the script to >> export the canvas as postscript: >> >> self.canvas.postscript(file='/**__tmp/canvas.ps <http://canvas.ps>') >> >> >> >> Cheers, >> Thomas >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> >> >> > > -- > Thomas Holder > MPI for Developmental Biology > |