[Chimera-users] Fwd: chimera MAV

[Eric Pettersen]

Unfortunately that option doesn’t offer control over the exact amount of inter-block spacing, just whether there is some or none.  To change the size of the inter-block spacing, you would need to edit the Python code.  Namely <your Chimera>/share/MultAlignViewer/SeqCanvas.py, line 1271.  That line should be:

	self.blockGap = 15

You would change 15 to whatever value you prefer.  I believe the value is in pixels.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

P.S.  If you are on a Mac, then “<your Chimera>” is Chimera.app/Contents/Resources.


> On Feb 9, 2017, at 9:29 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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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