[Chimera-users] [Chimera-user] multi align viewer

[Jacqueline Vitali]

Thank you Eric and Elaine.  It works well.

If you also  put Preferences>Appearance>line separation 0 pixels and in the
info>region browser you remove color for border, the background colors of
all sequences merge with each other.

Jackie Vitali
Cleveland State University.

On Thu, Jun 24, 2021 at 7:20 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

>
>
> > On Jun 24, 2021, at 4:17 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Jackie,
> > There is no way to do it, really.  However, if you don't mind there
> being a separate box border for each sequence as shown in the attached
> image, there is a tedious way, as outlined below.  I blame Eric for
> mentioning this, but I took so long trying it I thought I'd might as well
> mention it:
> >
> > (1) in the Multalign Viewer menu, choose Preferences... Headers.  Set
> Conservation style: AL2CO and in AL2CO parameters, very low gap fraction
> (e.g. 0.01) so that only the fully populated columns will get a
> conservation value.
> >
> > (2) in ONE model, select only the residues that have a conservation
> value, which will select only its residues in fully populated columns and
> show them as a green selection region.  E.g. command: sel
> #0:/mavConservation
>
> Correction: do this selection in ALL of the models, e.g. command: sel
> :/mavConservation
> >
> > (3) Copy the selection region to make a new region (so that it won't go
> away when you deselect anything or change selection).  In Multalign Viewer
> menu, choose Info... Region Browser.  In the Region Browser click the
> "Chimera selection" entry and click the Copy button to make a new region.
> Then you can clear selection and use the little color squares in the dialog
> to change the inside and border colors of the new copy region as you like.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > <Screen Shot 2021-06-24 at 4.15.58 PM.png>
> >> On Jun 24, 2021, at 3:25 PM, Jacqueline Vitali <jackie.vitali at gmail.com>
> wrote:
> >>
> >> Hi Elaine,
> >>
> >> When you do match-->align in chimera, you create the MAV.  It has a
> coral region for the fully populated columns.  If you change the order of
> the sequences, it automatically disappears.  Is there a way to bring this
> region back?
> >>
> >> Thank you.
> >>
> >> Jackie Vitali
> >> Cleveland State University
> >
>
>
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