VMD-L Mailing List

From: Ahmed Nawar (Ahmed.Nawar_at_bibalex.org)
Date: Tue Nov 27 2007 - 01:00:42 CST

Thanks,

  I solve My problems and the solution is:

1- Compile the VMD with the freevr option on "configure.options".
2- Install VMD
3- Run the VMD using VMD script (Normal Run)
4- If it is running correctly Run VMD with "-dispdev freevr". (vmd -dispdev freevr)
5- Else use "-debug" so you can debug and see the errors.(vmd -debug)
6- If you succeed you will see a Freevr simulation environment box, wand as triangle , and head tracker as box.
7- Configure ".vmdsensors" File by add or activate This lines
     device freevrtracker freevrtracker://local/freevr
     scale 1.0
     offset 0.9 -4.0 -1.0
     device freevrbuttons freevrbuttons://local/freevr:0,1,2,3

8- From menu (Graphics->Tools) create grab Tool And Set the "Tool Devices"
     Position: freevrtracker
     Buttons: freevrbuttons

9- You will see a tool and you will move it with the freevr simulated wand.
     Press "w" and use the arrows with "f" and "v" to move
     The mouse buttons will work as wand buttons.

10- To use the wand for moving the molecule you must target it by the position and mouse left button.
     This is very difficult so you could change the Drawing method to some thing big.

I hope this information can help any one.
And ofcourse If i am wrong in any thing please fix it.

Thanks for all replays.

Wait for "Bibliotecha Alexandrina" Results.

Ahmed Nawar
Software Developer
International School of Information Science (ISIS)
Bibliotecha Alexandrina
P.O. Box 138, El-Chatby Alexandria 21526, Egypt
Phone:+(203) 4839999, Ext.:1498
Fax:+(203) 482 0405
www.bibalex.org/isis
   

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Mon 11/26/2007 7:44 PM
To: Ahmed Nawar
Cc: Axel Kohlmeyer; VMD Mailing List
Subject: Suspected SpamFR:Re: vmd-l: cave
 

Hi,
  I don't have time to make a video on how to use VMD in FreeVR mode,
I'm afraid some patience and persistence will be required.
See the VMD User's Guide for information on how the .vmdsensors
file works, and how the Tools menu attaches to the devices defined in
that file. In your .vmdsensors file, you will need to have an entry
like this one for the FreeVR wand:

###
### Configuration for the FreeVR trackers
###
device freevrtracker freevrtracker://local/freevr
scale 1.0
offset 0.9 -4.0 -1.0
device freevrbuttons freevrbuttons://local/freevr:0,1,2,3

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 26, 2007 at 02:12:41PM +0200, Ahmed Nawar wrote:
>
> Thanks,
>
> I cannot compile the VMD without install tcl,netcdf and tk.
>
> It is run now .
>
> But What I Really need Are
> 1- Run VMD with FreeVR And I did.(Is This step was needing the compilation?)
> 2- Add a tool And use a mouse as a wand.
> - This step need a configuration (and ofcourse I can not use a mouse).
> - If I use the simulation wand in FreeVR. How can I use it to move the molecule.
> - The VMD not response to the mouse button(Is it?).
> - Is this simulation wand has the same function as a tool.
>
> I Need a movie for A running VMD With FreeVR. This may help me.
>
>
>
> Thanks
>
> Ahmed Nawar
> Software Developer
> International School of Information Science (ISIS)
> Bibliotecha Alexandrina
> P.O. Box 138, El-Chatby Alexandria 21526, Egypt
> Phone:+(203) 4839999, Ext.:1498
> Fax:+(203) 482 0405
> www.bibalex.org/isis
>
>
>
> -----Original Message-----
> From: akohlmey_at_gmail.com on behalf of Axel Kohlmeyer
> Sent: Mon 11/26/2007 12:28 PM
> To: Ahmed Nawar
> Cc: VMD Mailing List
> Subject: Suspected SpamFR:Re: Suspected SpamFR:RE: vmd-l: cave
>
> ahmed,
>
> On Nov 26, 2007 1:54 AM, Ahmed Nawar <Ahmed.Nawar_at_bibalex.org> wrote:
> >
> > Thanks for all replays,
> >
> > When I ran the VMD on debug mode I have a lot of warning all say
> >
> > "Warning) Rejecting plugin with incorrect ABI version: statically linked."
> >
> > I Compiled the source of 1.8.6 but i didn't found some packages as
> > tcl, tc , molfile so I get them from old on VMD 1.8.3 .
>
> you cannot use old molfile plugins with a new version of VMD.
> the whole set of plugins is distributed with the sources, and you
> have to compile them first. please check the instructions on how
> to compile VMD from sources more carefully. it is all documented.
>
> the current build system of VMD is optimized for portability and
> consistency across platforms, which mean, that most libraries are
> build for VMD in a separate directory and linked statically. if you
> want to use system libraries, you will have to adjust makefiles and
> flags. i'm doing this for fedora based machines and you may
> get some hints from the rpm spec files that are uploaded to the
> VMD biocore project.
>
> hope this helps,
> axel.
>
> >
> > If there is any thing wrong where I Can find a new and fully one to compile.
> >
> > thanks
> > Ahmed Nawar
> > Software Developer
> > International School of Information Science (ISIS)
> > Bibliotecha Alexandrina
> > P.O. Box 138, El-Chatby Alexandria 21526, Egypt
> > Phone:+(203) 4839999, Ext.:1498
> > Fax:+(203) 482 0405
> > www.bibalex.org/isis
> >
> >
> >
> > -----Original Message-----
> > From: Axel Kohlmeyer [mailto:akohlmey_at_cmm.chem.upenn.edu]
> > Sent: Sun 11/25/2007 8:58 PM
> > To: Ahmed Nawar
> > Cc: VMD Mailing List
> > Subject: Suspected SpamFR:RE: vmd-l: cave
> >
> >
> >
> >
> > -----Original Message-----
> > From: Axel Kohlmeyer [mailto:akohlmey_at_cmm.chem.upenn.edu]
> > Sent: Sun 11/25/2007 8:58 PM
> > To: Ahmed Nawar
> > Cc: VMD Mailing List
> > Subject: Suspected SpamFR:RE: vmd-l: cave
> >
> > On Sun, 25 Nov 2007, Ahmed Nawar wrote:
> >
> > AN> Thanks for all replays,
> > AN>
> > AN> I Compiled the VMD with freevr and installed it.
> > AN> But when I start the vmd it is shutdown and i haven't the time to see any error.
> > AN>
> > AN> So I need an installation guide for VMD with FreeVR.
> > AN> And how can i found the error if the command window close (Ex:log file).
> >
> >
> > please check the VMD Linux release notes and try running
> > VMD in text mode and if that does not produce a problem
> > in debug mode with "vmd -debug" and then "run".
> >
> > that should produce some output that would give you
> > a hint of what happenend and what went wrong.
> >
> > cheers,
> > axel.
> >
> > AN>
> > AN> Thanks
> > AN>
> > AN> Ahmed Nawar
> > AN> Software Developer
> > AN> International School of Information Science (ISIS)
> > AN> Bibliotecha Alexandrina
> > AN> P.O. Box 138, El-Chatby Alexandria 21526, Egypt
> > AN> Phone:+(203) 4839999, Ext.:1498
> > AN> Fax:+(203) 482 0405
> > AN> www.bibalex.org/isis
> > AN>
> > AN> -----Original Message-----
> > AN> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > AN> Sent: Thu 11/22/2007 6:21 PM
> > AN> To: Ahmed Nawar
> > AN> Cc: vmd-l_at_ks.uiuc.edu
> > AN> Subject: Re: vmd-l: cave
> > AN>
> > AN>
> > AN> Hi,
> > AN> If you use the VMD with FreeVR you can run in "simulator" mode
> > AN> that allows the keyboard and mouse to emulate the full CAVE environment,
> > AN> by letting you manipulate the positions and orientations of the wand
> > AN> and head tracker and so on. If you need to test on a desktop, that's
> > AN> the best way to go.
> > AN>
> > AN> Cheers,
> > AN> John Stone
> > AN> vmd_at_ks.uiuc.edu
> > AN>
> > AN> On Thu, Nov 22, 2007 at 02:09:24PM +0200, Ahmed Nawar wrote:
> > AN> > Dear All;
> > AN> >
> > AN> > We have a cave system.
> > AN> > I need to test my work on my pc before i go to the cave.
> > AN> > So i need a tool but i haven't any spatial device on my pc.
> > AN> > Is there any thing i can use to build a tool using the keyboard/mous.
> > AN> >
> > AN> > Thanks,
> > AN> > Ahmed Nawar
> > AN> > Software Developer
> > AN> > International School of Information Science (ISIS)
> > AN> > Bibliotecha Alexandrina
> > AN> > P.O. Box 138, El-Chatby Alexandria 21526, Egypt
> > AN> > Phone:+(203) 4839999, Ext.:1498
> > AN> > Fax:+(203) 482 0405
> > AN> > www.bibalex.org/isis
> > AN>
> > AN>
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> >
> >
> >
>
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 

-- 
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