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

[Elaine Meng]

Hi Jackie,
Wow, that's great!  I'm impressed by your diligence.   :-)
Elaine

> On Jun 24, 2021, at 11:46 PM, Jacqueline Vitali <jackie.vitali at gmail.com> wrote:
> 
> 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
> > 
>