[Chimera-users] Command line change active to show models
Jean-Didier Maréchal
jeandidier.marechal at uab.es
Fri Apr 18 07:25:17 PDT 2008
Hi everyone,
I was wondering if it was possible to change the "Active models" list
that lays below the command line, to a "showed models" list. I know that
I can pilot this through the model panel, however, I think that, for the
work I do, a direct access to this option would be more useful.
Thanks a lot,
JD
On Thu, 2008-04-17 at 12:00 -0700, chimera-users-request at cgl.ucsf.edu
wrote:
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> Today's Topics:
>
> 1. CHIMERA script for CONSURF (Fabian Gmail)
> 2. History feature for command line between sessions (Boaz Shaanan)
> 3. Re: CHIMERA script for CONSURF (Elaine Meng)
> 4. Re: CHIMERA script for CONSURF (Elaine Meng)
> 5. Re: CHIMERA script for CONSURF (Eric Pettersen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Apr 2008 10:11:42 +0300
> From: Fabian Gmail <fabian.glaser at gmail.com>
> Subject: [Chimera-users] CHIMERA script for CONSURF
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <4806F82E.7010605 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
> --
> 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
>
> Web: http://bku.technion.ac.il
> Email: fglaser at tx.technion.ac.il
> Tel: +972-(0)4-8293701
> Cel: +972-(0)54-4772396
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 17 Apr 2008 08:52:31 GMT
> From: Boaz Shaanan <bshaanan at bgu.ac.il>
> Subject: [Chimera-users] History feature for command line between
> sessions
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <f652ac011b292.48070fcf at bgu.ac.il>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> ?The history of commands in the command line mode is retained within a session and is very convenient but I was wondering whether there is a feature that will allow you to recall commands from previous sessions (such as in O for example - it generates an .o-history file which is being constantly updated and is very convenient). If not, is it possible to request the addition of such a feature ? There are many ways to implement this of course and I'm sure you'll find the best way, if it's not already there lurking in Chimera.
>
> ?? Cheers,
>
> ????????????? Boaz
>
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220 ; Fax: 646-1710
> Skype: boaz.shaanan?
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> ------------------------------
>
> Message: 3
> Date: Thu, 17 Apr 2008 10:25:27 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] CHIMERA script for CONSURF
> To: Fabian Gmail <fabian.glaser at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <5DEE6CC8-3FC2-4A1E-B40D-7894E3CAB092 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> 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
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 17 Apr 2008 11:14:19 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] CHIMERA script for CONSURF
> To: Fabian Gmail <fabian.glaser at gmail.com>
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <31C50A56-94F0-4149-AFF2-C3FC28DD2F8C at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Hi Fabian,
> I had failed to notice you are one of the ConSurf developers, so my
> reply focused more on what an outside user could do. However, if you
> are thinking of providing Chimera scripts from the server, that would
> be great!!
>
> If so, you probably do want discontinuous coloring with exactly the
> same colors and sets of residues, so that all the graphics programs
> would show the same thing.
>
> Thus the Chimera script should contain "colordef" to define the
> colors and "color" to apply them to the residues. There are
> different possibilities for specifying the residues in the color
> command, however.
>
> (a) simply specify the residues by their residue numbers, like in the
> Consurf rasmol scripts
>
> (b) use "alias" to name sets of residues and then specify the
> residues by the alias string
>
> (c) make an attribute definition file (this file is read using the
> command "defattr") and then specify residues by attribute value.
> Disadvantage is an extra file. Advantages are that the Chimera
> script could stay the same and only a new attribute definition file
> made for each structure, and that a user could later decide to use a
> different coloring scheme for the attribute. Both the normalized
> score attribute and the 1-9 category score could be assigned in the
> same file.
>
> I can provide more details on any of these if you would like. Sorry
> about the length of the previous mail - I was trying to cover all the
> possibilities since I wasn't sure what you wanted!
> 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
>
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 17 Apr 2008 11:24:16 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] CHIMERA script for CONSURF
> To: Elaine Meng <meng at cgl.ucsf.edu>
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <FD6612CF-2D00-4F94-BF78-164DA17F0CDD at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> If the conservation scores are already in the b-factor field of the
> PDB, then you can skip the defattr part and use commands like:
>
> color red @/bfactor>3.0 & @/bfactor<=4.0
>
> to color atoms.
>
> --Eric
>
> On Apr 17, 2008, at 11:14 AM, Elaine Meng wrote:
>
> > Hi Fabian,
> > I had failed to notice you are one of the ConSurf developers, so my
> > reply focused more on what an outside user could do. However, if you
> > are thinking of providing Chimera scripts from the server, that would
> > be great!!
> >
> > If so, you probably do want discontinuous coloring with exactly the
> > same colors and sets of residues, so that all the graphics programs
> > would show the same thing.
> >
> > Thus the Chimera script should contain "colordef" to define the
> > colors and "color" to apply them to the residues. There are
> > different possibilities for specifying the residues in the color
> > command, however.
> >
> > (a) simply specify the residues by their residue numbers, like in the
> > Consurf rasmol scripts
> >
> > (b) use "alias" to name sets of residues and then specify the
> > residues by the alias string
> >
> > (c) make an attribute definition file (this file is read using the
> > command "defattr") and then specify residues by attribute value.
> > Disadvantage is an extra file. Advantages are that the Chimera
> > script could stay the same and only a new attribute definition file
> > made for each structure, and that a user could later decide to use a
> > different coloring scheme for the attribute. Both the normalized
> > score attribute and the 1-9 category score could be assigned in the
> > same file.
> >
> > I can provide more details on any of these if you would like. Sorry
> > about the length of the previous mail - I was trying to cover all the
> > possibilities since I wasn't sure what you wanted!
> > 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
> >
> >
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
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>
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