[Chimera-users] Fwd: chimera MAV

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 9 09:29:32 PST 2017


Hi Jackie,
Yes, see the sequence window menu: "Preferences… Appearance. " There are several options for spacing, font, and coloring, including “Space between wrapped blocks.”

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavprefs>

Best,
Elaine

> On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <jackie.vitali at gmail.com> wrote:
> 
> Elaine,
> 
> Thank you so much.  Doing it by hand is the easiest.  
> Also, is there a way to increase the distance between wrapped blocks? 
> 
> Jackie Vitali
> Cleveland State University
> 
> On Wed, Feb 8, 2017 at 1:39 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> You can also:
> 
> (1) hide/show the header lines (Conservation, Consensus, etc.) using the sequence window Headers menu
> (2) change how Conservation is calculated (sequence window Preferences… Headers)
> (3) add your own headers with quantities or symbols, e.g. put stars over the columns with superfamily-conserved residues
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>
> 
> Elaine
> 
> > On Feb 8, 2017, at 8:30 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Jackie,
> > You can draw boxes (we call them “regions”)  in the alignment wherever you want with click and drag, and then change their colors using the Region Browser.
> >
> > Multalign Viewer:
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
> >
> > Regions, including how to create them manually:
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regions>
> >
> > Region Browser (click the square color wells to change colors):
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regionbrowser>
> >
> > I hope this helps,
> > Elaine
> >
> >
> >> On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali at gmail.com> wrote:
> >>
> >> Elaine,
> >>
> >> I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV?  I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top.  But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color.  In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way.
> >>
> >> I hope my question is clear.
> >>
> >> Thank you in advance.
> >>
> >> Jackie Vitali
> >> Cleveland State University
> 
> 




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