Re: [Chimera-users] Fwd: chimera MAV
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/mu...> Best, Elaine
On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <jackie.vitali@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@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/mu...>
Elaine
On Feb 8, 2017, at 8:30 AM, Elaine Meng <meng@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/fr...>
Regions, including how to create them manually: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu...>
Region Browser (click the square color wells to change colors): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu...>
I hope this helps, Elaine
On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali@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
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@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/mu...>
Best, Elaine
On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <jackie.vitali@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@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/mu...>
Elaine
On Feb 8, 2017, at 8:30 AM, Elaine Meng <meng@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/fr...>
Regions, including how to create them manually: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu...>
Region Browser (click the square color wells to change colors): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu...>
I hope this helps, Elaine
On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali@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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participants (2)
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Elaine Meng -
Eric Pettersen