[Chimera-users] Chimera-users Digest, Vol 135, Issue 20

Boaz Shaanan bshaanan at bgu.ac.il
Mon Jul 21 13:50:36 PDT 2014


Hi,

On top of what Elaine wrote there is also the interface between Consurf (http://consurf.tau.ac.il/) and Chimera, which is also a very nice option.

   Cheers,

              Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





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From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] on behalf of chimera-users-request at cgl.ucsf.edu [chimera-users-request at cgl.ucsf.edu]
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Subject: Chimera-users Digest, Vol 135, Issue 20

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Today's Topics:

   1. surface color by conservation among different     sequences (???)
   2. Re: surface color by conservation among different sequences
      (Elaine Meng)


----------------------------------------------------------------------

Message: 1
Date: Mon, 21 Jul 2014 23:20:45 +0800
From: ??? <21620101152414 at stu.xmu.edu.cn>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] surface color by conservation among different
        sequences
Message-ID: <211F19AF-2CA8-4E66-81D4-0F9BC20A868A at stu.xmu.edu.cn>
Content-Type: text/plain; charset="us-ascii"

Hi,
I want to show a model in surface style which represents the conservation based on a series of sequences by its color.  I have got a result of sequence alignment (.fas file).
How can I apply this alignment result to the surface coloring  in Chimera?
Thanks!

best wishes!

Zhihai Li
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Message: 2
Date: Mon, 21 Jul 2014 09:37:53 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: ??? <21620101152414 at stu.xmu.edu.cn>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] surface color by conservation among
        different       sequences
Message-ID: <A6CEC949-E169-485A-93EE-3E3CD228730D at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8

Hi Zhihai,
There is an example near the end of this tutorial <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
...but I'll outline the steps here:

(1) open the sequence alignment (I would first rename the file to .fa or .fasta since those are recognized by Chimera). You can just use the main menu: File? Open.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment>

(2) open the structure, hide atoms, show surface (e.g. menu: Actions? Atoms/Bonds? hide, Actions.. Surface? show).   Of course, if you want to show some atoms such as a ligand, you could do that.

(3) check if the structure is associated with a sequence in the alignment.  A colored rectangle will appear behind the name of the sequence that is associated.  If there is a sequence that matches or almost-matches the sequence of the structure, it should happen automatically, but if not, you can force it using the Multalign Viewer (sequence window) menu: Structure? Associations.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association>

(alternatively, another possibility is to add the sequence of your structure to the alignment, see Multalign Viewer menu: Edit? Add Sequence)

(4) in the Multalign Viewer window, there is a Conservation histogram above the sequences.  Choose how you want to calculate these values with Multalign Viewer menu: Preferences? Headers.   In those preferences change "Conservation style" to "AL2CO" and then many more options will appear, allowing you to choose the type of equation (entropy, variability, etc.), sequence weighting, and smoothing window width.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavpref-analysis>

(5) again from Multalign Viewer menu: Structure? Render by Conservation.  This will call the Render by Attribute tool in which you can interactively choose the colors and how they map to the values.  The conservation values from Multalign Viewer will be the "residue" attribute named "mavConservation".  You can try different colorings, and you can go back to #4 above and change the method, then "Refresh? Values" in the Render by Attribute tool to update with the new values.  When you get the coloring you like, you can turn on the option to create a color key for your figure.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 21, 2014, at 8:20 AM, ??? <21620101152414 at stu.xmu.edu.cn> wrote:

> Hi,
> I want to show a model in surface style which represents the conservation based on a series of sequences by its color.  I have got a result of sequence alignment (.fas file).
> How can I apply this alignment result to the surface coloring  in Chimera?
> Thanks!
> best wishes!
> Zhihai Li




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