VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 15 2006 - 18:59:20 CST

Hi,
  You can change the color scale min/midpoint/max values with the
"color scale xxx" commands:
   http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node109.html

Which version of VMD are you using? The not updating issue is a bug
caused by an update event not being sent (or not being honored) somewhere
in the scripting interface, and so I'll need to track that down if it's
one we haven't already fixed in the test versions of VMD 1.8.4.
In the mean time, you can try making the "color scale" commands the
last ones in the script, as they should force the update, even if
the various scaleminmax stuff did not. If that still doesn't work,
I'll need to see the exact script you're using in order
to determine why the update isn't happening.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 15, 2006 at 02:54:58PM -0600, Jeffrey Tseng wrote:
> John,
> I have tried different commands such like 'display update ui|on|off'
> but the colors of figure dosen't change correspondingly.
>
> After running my script, I have to go to "Graphical Representations" menu
> to push the button of "Apply Changes Automatically" for updating the
> colorings.
>
> I notice that when I push the button "Apply Changes Automatically" , the VMD
> re-runnig the "surf" repsentation showing in the monitor.
>
> Also, in the "Color Controls" menu, there is a "offset bar" under the tab
> of "Color Scale". Every time, I move the bar of "offset". The colors of the
> figure change dynamically. I wonder how do you use the script command to
> change it.
>
> Could you show the "command" to change the value "offset" in the color scale
> RGB ?
>
>
>
> Since you help accomplish this figure so much, I would like to acknowledge
> you in the paper published. Would you mind telling me how to summit this
> figure to KS website when it is done?
>
> As I said , it can't not be fully automatically generated because every
> time I have to push the button of "Apply Changes Automatically".
>
> Cheers,
>
> -Jeffrey
>
>
>
>
>
>
>
>
>
>
>
> On 3/15/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> > 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
> > 

-- 
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