VMD-L Mailing List

From: MyLinkka (mylinkka_at_gmail.com)
Date: Fri May 29 2009 - 05:15:26 CDT

Hi, John,

Thank you for the instruction! I've tried them. Here feed back some results.

1. As you suggested, the default colors can be easily modified in the
startup file.
It worked perfectly. But I'm still curious about why you chose cyan as
default for carbon.:)

2. Python. Never mind. Tcl is fine. one just needs to remember some more
keywords if he
knows programming. For beginers GUI is enough.

3. Positioning the windows. On my Windows PC, the 'menu' command can
handle the position
of any window or dialogbox but the OpenGL display window. I cannot find
a way to
move the OpenGL window. I fond some startup command line options which
can modify
this window, like '-size 800 600'. But again the command line '-pos 200
300' doesn't work.
The OpenGl display window always sits at 0,0 on my screen unless I move
it manually. So
'auto-layout' plan seems not working here. What I do now is leave the GL
window as it is
but move the main window and other dialogs out of the region of GL
window. At least in this way
I don't have to move the main window each time when I start vmd. But the
console window
is still overlapped with the GL window and I cannot find a command to
move it. Maybe this is
because vmd doesn't wrap the console as internal command input, it still
a normal system console.
However, I believe it can be done on any OS.

BTW, vmd 1.8.7 beta 3 still doesn't work on my notebook (Nivdia Quadro
2700M with the latest
driver from Nvidia website, Windows XP pro, HP notebook 8730w, Intel®
Core™2 Extreme quad-core)
i notice their is an command line option '-debug'. Where can I find the
debug version for Windows?
I would like to fix this problem.

Ting

John Stone wrote:
> Hi,
> I thought I'd answer a couple of the questions you had about
> customizing the behavior of VMD, though Axel already addressed
> some aspects of your questions previously:
>
> On Wed, May 20, 2009 at 02:11:35PM +0200, MyLinkka wrote:
> [...]
>
>> 1. The default colors. In my very personal opinion, the default colors
>> for atoms are 'unusual'.
>>
>
> You can customize this as you see fit. There are two approaches
> for doing this:
>
> 1) edit the $install_dir/vmd/scripts/vmd/colordefs.dat to modify the
> default behavior of the program system-wide, e.g. editing the top
> portion of the colordefs.dat file:
>
> #
> # VMD default color assignments
> #
> # color category name, category item name, color name
> #
> Name H white
> Name O red
> Name N blue
> Name C cyan
> Name S yellow
> Name P tan
> Name Z silver
> [....]
>
> 2) modify the colors in your own .vmdrc file, by adding new lines.
> Copy $install_dir/vmd/.vmdrc to .vmdrc (on unix) or vmd.rc (on windows)
> as a starting point, and then add lines like this one:
> color Name C gray
>
>
>
>> 2. Python support on windows.
>>
>
> At present, this can't be supported in the precisely same way we can for
> the other platforms, due to the architecture of Python itself, as
> described in the Python documentation here:
> http://www.python.org/doc/faq/windows/#how-can-i-embed-python-into-a-windows-application
> http://www.faqts.com/knowledge_base/view.phtml/aid/5325
>
> That said, I am looking to work around this problem by changing the VMD
> distribution to accomodate Python's linkage requirements, but it's
> not going to be easy and it won't be done for VMD 1.8.7.
>
>
>> 3. Window layout. I know there is some tradition for L(u)nix software
>> that many separated
>> and modeless windows belong to one program. Normally on windows, in this
>> case
>> a program will create some child windows. (if you check what gimpshop
>> project (and gimp)
>> does, probably you will understand this. ) Vmd works in the unix way.
>> But one annoying
>> thing is, each time when I start vmd, all windows (console, gl and main
>> window) are overlapped
>> (at the upper-left corner of my screen). I have to manually move and
>> rearrange them in
>> order to see all of them. (maybe this could be controlled in the startup
>> file?)
>>
>
> You can manipulate the location of any of the built-in menus in VMD with the
> "menu" commands, e.g.:
>
> # position and turn on menus
> menu main move 5 225
> menu display move 395 30
> menu graphics move 395 500
> menu color move 125 225
> menu files move 125 325
> menu labels move 125 525
> menu render move 125 525
>
> menu main on
> menu display off
> menu graphics on
> menu color off
> menu labels off
> menu render off
> menu files off
>
> Please try out these suggestions and let me know if you have
> further questions.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>