VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 15 2006 - 10:09:46 CST

Oops, missed the bottom of your email:
  That's actually not very easy to do, because there's not a good way of
assigning a specific RGB color to a specific piece of atom-associated
geometry with the current system. The most obvious method to get it done,
though as I say is not ideal, is to rewrite the color scale with your own
values using a script and assign the color scale data range so you can
predict the mapping of beta/user/occupancy/etc values to RGB colors.
There's an example in the VMD User's Guide with a little Tcl script
the redefines the color scale colors. Let me know if you need help with that.

I'm working on writing a better coloring scheme to handle this problem at
the request of a number of people, but I don't have anything ready yet,
so this hack will have to do for the short term.

  John Stone
  vmd_at_ks.uiuc.edu

> Also, how do we "correctly" assign the "specific" color to the subselection.
> like,
> The command you gives me:
>
> color scale method RWB
>
> It seems the colors are predefined. I could not do too much about color
> assignments.
>
> Is there any way to correctly assign the desired color to the selection
> when we use the "User" color method ?
>
>
> Again, thanks so much for your help.
>
>
> -Jeffrey
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On 3/14/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> > Hi,
> > So using your example you'd do something like this:
> >
> > atomselect macro otherselect { resname ASN and resid 273 and name OD1
> > or resname ASP and resid 269 and name OD2
> > or resname ASP and resid 269 and name OD1
> > or resname ASP and resid 269 and name CG }
> >
> > set sel1 [atomselect top "myselect"]
> > set sel2 [atomselect top "otherselect"]
> >
> > # sets everything to zero
> > $sel1 set user 0.0
> >
> > # set just those other four differently
> > $sel2 set user 1.0
> >
> > mol modcolor 0 0 User
> > mol scaleminmax 0 0 0.000000 1.000000
> > color scale method RWB
> >
> > $sel1 delete
> > $sel2 delete
> >
> >
> >
> > On Tue, Mar 14, 2006 at 03:18:32AM -0600, Jeffrey Tseng wrote:
> > > Hi, John,
> > > I do need a method that assigns values to the per-atom data fields
> > such
> > > as "user" or "occupancy" instead of beta.
> > >
> > > ( Using "beta" dosen't fit my needs for some other reasons )
> > >
> > >
> > > Here is the example:
> > > ###############################
> > > mol representation SURF 1.4
> > > atomselect macro myselect {
> > > resname ASN and resid 273 and name OD1
> > > or resname ASP and resid 269 and name OD2
> > > or resname ASP and resid 269 and name OD1
> > > or resname ASP and resid 269 and name CG
> > > or resname HIS and resid 268 and name NE2
> > > or resname LEU and resid 210 and name CD1
> > > or resname LEU and resid 210 and name CG
> > > or resname LEU and resid 210 and name CB
> > > or resname LEU and resid 210 and name N
> > > }
> > >
> > > mol selection {myselect}
> > > mol addrep top
> > >
> > > ######## Here is the subselction; the subsubselect is just the frist 4
> > atoms
> > > of myselect ###############
> > >
> > >
> > > mol selection {
> > > resname ASN and resid 273 and name OD1
> > > or resname ASP and resid 269 and name OD2
> > > or resname ASP and resid 269 and name OD1
> > > or resname ASP and resid 269 and name CG
> > > }
> > >
> > >
> > > ###########################
> > >
> > > How do we use the "user" or "occupancy" data fields to color different
> > > selections, saying that the first selection is colored
> > "green" and the
> > > rest of them (subselection) is colored "red" ?
> > >
> > >
> > > Thanks,
> > >
> > > -Jeffrey
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On 3/14/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> > > >
> > > >
> > > > Jeff,
> > > > The example you cite was simply colored by atom name. Because surf
> > > > doesn't assign atom IDs to each vertex in the surface, whole facets
> > are
> > > > colored by atom properties, which results in a fairly coarse coloring
> > > > of the surface. You can do this sort of thing quite easily though,
> > like
> > > > this (say you had 100 atoms for example):
> > > > set sel1 [atomselect top "index 0 to 50"]
> > > > set sel2 [atomselect top "index 51 to 99"]
> > > > $sel1 set beta 1.0
> > > > $sel2 set beta 2.0
> > > > $sel1 delete
> > > > $sel2 delete
> > > >
> > > > You could just as easily have made the selections something else:
> > > > set sel1 [atomselect top "x > 0"]
> > > > set sel2 [atomselect top "x < 0"]
> > > >
> > > > Then set the rep coloring mode to "beta" and use the color scale
> > > > data range and color scale controls to tweak if necessary.
> > > > Do you need more of an example than this or does this make it clear?
> > > >
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Mon, Mar 13, 2006 at 02:12:09PM -0600, Jeffrey Tseng wrote:
> > > > > Hi, John
> > > > > Thanks for your quick responding and helpful comments.
> > > > >
> > > > > Yes, you are right. If I split the selection into parts. The
> > > > > reprensentation is not what I want.
> > > > >
> > > > >
> > > > > I would like to try the other way that you suggest, which is to use
> > > > per-atom
> > > > > data fields such as "user" or "occupancy".
> > > > >
> > > > > Could you please use my example I gave in the previous email to show
> > how
> > > > to
> > > > > color different selections of the same repesentation?
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Also, I found that in KS website, there is one example. It looks
> > like a
> > > > > perfect example.
> > > > > Here is link.
> > > > > http://www.ks.uiuc.edu/Research/vmd/allversions/repimages/surf.jpg
> > > > > If you know how to generate it, I wonder if the vmd script is
> > > > available.
> > > > >
> > > > > Thanks a lot,
> > > > >
> > > > > -Jeffrey
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On 3/13/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> > > > > >
> > > > > >
> > > > > > Hi,
> > > > > > A representation can only have one coloring method active at a
> > time.
> > > > > > If you use the ColorID coloring method, then that eliminates the
> > > > > > possibility
> > > > > > of having two colors at once for a given selection. You could
> > either
> > > > > > split
> > > > > > your atom selection into two parts and make one representation for
> > > > each,
> > > > > > coloring them differently (which may not work very well for your
> > Surf
> > > > > > representation), or you can assign values to one of the per-atom
> > > > > > data fields such as "user", "beta", "occupancy", etc, and then
> > color
> > > > > > by that data field rather than by ColorID. Let me know if you
> > need
> > > > > > more help with this.
> > > > > >
> > > > > > John Stone
> > > > > > vmd_at_ks.uiuc.edu
> > > > > >
> > > > > > On Sun, Mar 12, 2006 at 02:52:15PM -0600, Jeffrey Tseng wrote:
> > > > > > > Hi,
> > > > > > >
> > > > > > > Is it possible to change the color of subset of the selection
> > ?
> > > > > > >
> > > > > > > Here is an example:
> > > > > > > ###########################
> > > > > > > mol representation SURF 1.4
> > > > > > > atomselect macro myselect {
> > > > > > > resname ASN and resid 273 and name OD1
> > > > > > > or resname ASP and resid 269 and name OD2
> > > > > > > or resname ASP and resid 269 and name OD1
> > > > > > > or resname ASP and resid 269 and name CG
> > > > > > > or resname HIS and resid 268 and name NE2
> > > > > > > or resname LEU and resid 210 and name CD1
> > > > > > > or resname LEU and resid 210 and name CG
> > > > > > > or resname LEU and resid 210 and name CB
> > > > > > > or resname LEU and resid 210 and name N
> > > > > > > }
> > > > > > >
> > > > > > > mol selection {myselect}
> > > > > > > mol color colorID 12
> > > > > > > mol addrep top
> > > > > > >
> > > > > > > ########################################
> > > > > > >
> > > > > > > Now myselect will be colored "green" surface.
> > > > > > >
> > > > > > >
> > > > > > > Here is the subselction
> > > > > > >
> > > > > > > mol selection {
> > > > > > > resname ASN and resid 273 and name OD1
> > > > > > > or resname ASP and resid 269 and name OD2
> > > > > > > or resname ASP and resid 269 and name OD1
> > > > > > > or resname ASP and resid 269 and name CG
> > > > > > > }
> > > > > > >
> > > > > > >
> > > > > > > I would like to make the subselection colored "red" and the
> > surface
> > > > > > > representation can not be changed.
> > > > > > >
> > > > > > > Is there any good way to make this task happen ?
> > > > > > >
> > > > > > >
> > > > > > > Thanks in advance.
> > > > > > >
> > > > > > > -Jeffrey
> > > > > >
> > > > > > --
> > > > > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > > > Beckman Institute for Advanced Science and Technology
> > > > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > > > > >
> > > >
> > > > --
> > > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > Beckman Institute for Advanced Science and Technology
> > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > > >
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078