VMD-L Mailing List

From: Paweł Wolski (pawl.wolski_at_gmail.com)
Date: Wed Oct 01 2014 - 02:26:59 CDT

Thank you all for your reply.
now I know how do it

Best,
Pawel

2014-09-30 21:22 GMT+02:00 Josh Vermaas <vermaas2_at_illinois.edu>:

> Hi Pawel,
>
> Fundamentally, it comes down to an assumption VMD makes when it comes down
> to coloring things by name. In general, the assumption is that we want to
> see all atoms of the same element have the same name. For proteins, which
> have all their carbons with names like "CA CB CC, etc.", we see that only
> the first character matters in letting VMD guess that its a carbon atom.
> VMD doesn't let you set these independently if that's what you want without
> some trickery (if you use the command "color add item Name CA green", CA
> atoms will still be cyan, not green for instance, because it matches with
> the C first before encountering CA in the color list). For you, the same
> logic means that VMD wants to treat 1, 10, 11, 12, 13, 14 and 15 as one
> element when you want them to be 7 separate ones. What I do is to rename
> things so that VMD cannot try and be clever. For you, that means the
> following:
>
> $core set name A
> $Hchain set name B
> $d set name C
> $Pt set name D
> $cptN set name E
> $Cl set name F
> $cptH set name G
>
> color Name A magenta
> color Name B green
> color Name C red
> color Name D yellow
> color Name E blue
> color Name F green
> color Name G red
>
> This will do exactly what you want it to, at the cost of you needing to
> rename some atoms. This isn't scalable, and I think you are manually doing
> what a datastructure with atomnames rather than numbers would do
> automatically. Is your input convertable to pdb or something first so that
> the atomnames will be more meaningful than just plain numbers and VMD's
> guessing will work to your benefit?
> -Josh Vermaas
>
>
> On 09/30/2014 01:08 PM, Paweł Wolski wrote:
>
> Hi
>
> In VMD -> Graphics -> Colors... -> Categories
> I don't have "10".
> I'm tryinf to run a script. Script look like this:
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> * mol load lammpstrj k165r1.lammpstrj color Display Background white set
> CNT [atomselect top "name 1"] set CA [atomselect top "name 2"] set MNP
> [atomselect top "name 3"] set Opeg [atomselect top "name 4"] set core
> [atomselect top "name 11"] set Si [atomselect top "name 5"] set Cchain
> [atomselect top "name 6"] set OA [atomselect top "name 7"] set HA
> [atomselect top "name 8"] set N [atomselect top "name 9"] set Hchain
> [atomselect top "name 10"] set d [atomselect top "name 33"] set Pt
> [atomselect top "name 12"] set cptN [atomselect top "name 13"] set Cl
> [atomselect top "name 14"] set cptH [atomselect top "name 15"]*
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> *$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?
>
>
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> 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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