VMD-L Mailing List
From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Tue Sep 30 2014 - 13:39:15 CDT
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Pawel,
Absence of "10" in Name subcategory coincides with Axel's explanation.
Can you color your atoms not based on atom names but on something else?
Maxim
On Sep 30, 2014, at 1:08 PM, Paweł Wolski <pawl.wolski_at_gmail.com> wrote:
> Hi
>
> In VMD -> Graphics -> Colors... -> Categories
> I don't have "10".
> I'm tryinf to run a script. Script look like this:
>
> mol load lammpstrj k165r1.lammpstrj
>
> color Display Background white
>
> set CNT [atomselect top "name 1"]
> set CA [atomselect top "name 2"]
> set MNP [atomselect top "name 3"]
> set Opeg [atomselect top "name 4"]
> set core [atomselect top "name 11"]
> set Si [atomselect top "name 5"]
> set Cchain [atomselect top "name 6"]
> set OA [atomselect top "name 7"]
> set HA [atomselect top "name 8"]
> set N [atomselect top "name 9"]
> set Hchain [atomselect top "name 10"]
> set d [atomselect top "name 33"]
> set Pt [atomselect top "name 12"]
> set cptN [atomselect top "name 13"]
> set Cl [atomselect top "name 14"]
> set cptH [atomselect top "name 15"]
>
> $CNT set radius 0.849917
> $CA set radius 0.849917
> $MNP set radius 50.000000
> $core set radius 50.000000
> $Opeg set radius 0.750000
> $Si set radius 0.750000
> $Pt set radius 0.914750
> $cptN set radius 0.844575
> $Cl set radius 1.156800
> $cptH set radius 0.617838
> $Cchain set radius 0.849917
> $d set radius 5.000000
> $OA set radius 0.739980
> $HA set radius 0.534540
> $N set radius 0.812500
> $Hchain set radius 0.617838
>
> color Name 8 green
> color Name 10 green
> color Name 1 gray
> color Name 2 gray
> color Name 6 gray
> color Name 4 red
> color Name 7 red
> color Name 5 black
> color Name 12 yellow
> color Name 13 blue
> color Name 14 green
> color Name 15 red
> color Name 9 blue
> color Name 3 yellow
> color Name 33 red
> color Name 11 magenta
>
> when i run it, I get error: Unable to change color name. when I delete command with 10,11,12,13 ...
> everything works well
> what is wrong?
>
>
>
> 2014-09-30 18:08 GMT+02:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> On Tue, Sep 30, 2014 at 10:54 AM, Paweł Wolski <pawl.wolski_at_gmail.com> wrote:
> > Hi,
> >
> > I have problem with change atoms colors when it's name have two chars, eg:
> > when I use command:
> > color Name 1 gray
> > - everything is ok, by when I use:
> > color Name 10 gray
> > I get error: Unable to change color name.
> > In this structure I have atom's name 10.
> > What I do wrong?
>
> nothing.
>
> however VMD limits how strings are recognized in the Name field for
> most entries to the first character. this has its origin in the custom
> that in PDB files atom names indicate their topological position with
> the second character (CA is alpha carbon, HA hydrogen at alpha carbon,
> CB is beta carbon as so on).
>
> axel.
>
> >
> > Best,
> > Pawel
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
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