[Chimera-users] CHIMERA script for CONSURF

[Fabian Glaser]

Dear Elaine,

This is very very useful and infomative, I meant indeed to use the
exact discontinued color-coding to write a script and offer it to
ConSurf users as an alternative to create high quality pictures.

Thanks a lot!

Fabian

On 17/04/2008, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> On Apr 17, 2008, at 12:11 AM, Fabian Gmail wrote:
> > Hi all,
> > I am very interested to write a script to deal with  the color-coding of
> > CONSURF server (http://consurf.tau.ac.il/index.html), a 9
> layer colour
> > from maroon-to-cyan. I basically would like to know how I could
> > translate the code into RGB colors and color the structure accordingly.
> >
> > Any suggestions will be greatly appreciated,
> > Fabian Glaser
> >
> >
> Hi Fabian,
> Do you mean you want to take the ConSurf results and show them in Chimera,
> using the same colors that the ConSurf Web server uses?  Or do you simply
> want to use that color scheme with conservation values or other properties
> calculated in Chimera?
>
> Either way, Chimera has some nice features for working with "attributes"
> (named properties with values).  First I'll describe attributes, then how to
> show their values with colors.  I will try to be brief, but there are many
> things that may be relevant!
>
> ATTRIBUTES
> Examples of attributes are atom B-factors read from a PDB file, and amino
> acid hydrophobicities.  Those are created automatically by Chimera, but you
> can create your own attributes arbitrarily using Define Attribute.  If you
> open a sequence alignment, a residue Conservation attribute is automatically
> added to the associated structure(s).  There are several options (entropy,
> variation, sum-of-pairs, with or without sequence weighting) for calculating
> the conservation attribute values.  That flexibility is why I thought you
> might want to use values calculated in Chimera.  It is very easy to just
> open your sequence alignment and structure; association is automatic.
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavAttributes
>
> COLORING
> When the structure has a numerical attribute of interest, you can map colors
> to the values with "Render by Attribute" (under Tools... Depiction) or the
> command "rangecolor."  The former has a graphical interface with a histogram
> of the values.  You can place several vertical bars on the histogram and
> give each a color to define the color mapping.  This is also very flexible
> and convenient.  Rangecolor does the same thing but without a graphical
> interface.  "Render by Attribute" can also show residue values with a "worm"
> (tube that varies in fatness).
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html
>
> One difference between coloring this way and with ConSurf is that the
> methods above will color continuously, shading from one color to another,
> whereas ConSurf colors discontinuously.  You could also color
> discontinuously with Chimera... more on that below.
>
> Just now I used the ConSurf server on PDB:2mnr, viewed the results in Jmol,
> and downloaded some results.   One result file is "PDB File with
> Conservation Scores in the tempFactor field."  Thus, you don't even have to
> use Define Attribute - if you just open that PDB file in Chimera you will
> already have the ConSurf scores available as the atom attribute "bfactor".
> Start "Render by Attribute" and show the "atom" attribute "bfactor" ... then
> change to "residue" and there will also be an attribute "average -> bfactor"
> (average of the atomic values).  Either way you have a histogram of values
> and can define a color mapping.  To color ribbons or show worms, you need to
> use the residue attribute, not the atom one.
>
> If I add two additional sliders to the histogram (Ctrl-click) and make the
> colors from left to right: violet red, hot pink, white, cyan, dark cyan, it
> is an approximate visual match to the ConSurf scheme.  Apparently negative
> scores reflect more conserved positions.  Of course, you are not limited to
> the named colors - you can generate whatever colors you want in the Color
> Editor - but it is easier to describe here, and you could also use those
> color names in a "rangecolor" command, for example:
>
> rangecolor bfactor,a,r -2 violet red -1 hot pink 0 white 1 cyan 2 dark cyan
>
> You can also create new color names with "colordef" and use those in
> "rangecolor."
>
> If you want the EXACT ConSurf colors, they are in the rasmol scripts from
> ConSurf.  Here is a rasmol color: [240,125,171]  To define the same color in
> Chimera, divide each number by 255, e.g. with the command:
>
> colordef mycol2 0.94 0.49 0.67
>
> If you want discontinuous coloring, you could either write a program to
> generate Chimera command scripts from the Consurf rasmol scripts or create
> an attribute assignment file (a simple text format)
> to assign a residue attribute with values 1-9 (or 0-9?) to match those
> ConSurf groups.
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile
>
> If converted rasmol script, the commands would then look something like
>
> colordef mycol2 0.94 0.49 0.67
> color mycol2 :140,143,164,168,105,117,122,126
>
> If you had defined/assigned a new residue attribute named conSurf, the
> commands would look something like
>
> colordef mycol2 0.94 0.49 0.67
> color mycol2 :/conSurf=2
>
> FINALLY, instead of using the ConSurf scores, you could just open the
> multiple sequence alignment from Consurf in Chimera (you can even load the
> tree from Consurf too!), open the structure, and work with the residue
> Conservation attribute as mentioned above.
>
> Phew! I hope this helps somebody!
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
>
>


-- 
___________________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

E-mail: fglaser at tx.technion.ac.il
Tel:    +972-4-829-3701
Cell:   +972-52-2357731