Subject: CCL: SUMMARY: Software to animate frequency calc

From: "Donald Keidel" <[email-masked]>
Date: Mon, 28 Apr 2003 11:07:07 -0700

Hello all,

I want to thank everyone who responded to my request for information.
All responses were very helpful.  Thank you all again.

I think Molden can do this as a series of gifs.

-Cory 

"Molden" (available for nearly all platforsm, although UNIX is supported
best) can read g98-outputs and animate the frequencies. A movie can't be
saved, as far as I remember....

but

xmakemol and xvibs together are nearly perfect:

xvibs extracts the  normal modes from a g98 output

(avbailable as src code, infos in the header) and puts them in *.xyz
files, 

that can be read from (beside molden and much other programs) by
xmakemol (LINUX tool, available as src, bin, rpm, deb,...), which has
the possibility to save animations. It creates *.xpm files, which 

can be concatenated together to become an mpeg or animated gif file. I
guess the "Help" function or webpage woll tell more....

All software is best found by a www search with e.g. "www.google.com".

If you can't find something, let me know and I'll help you.

Bye

Elmar

I use molekel to create rendered frames from g98 output, and then some 

sgi tools to convert them into a movie. 

The molekel people have done the same thing here:
http://www.cscs.ch/molekel/gallery.html

You could probably find free tools or write scripts to catenate and 

convert from image frames to a movie format if you don't have this 

already; here for example: http://www.gnu.org/directory/graphics/anim/

Or by screen capture while molekel is playing: 

http://www.gnu.org/directory/vid/

Molekel has a reputation for beautiful rendering and ease of use. If you
find a handier or more attractive solution, please let me know.

Hope this helps,

Jeremy

Hi,

I have used Jmol 

http://jmol.sourceforge.net/

to visualize vibrational motion.

Best regards,

Per-Olof Åstrand

Molden can animate frecuencies and you can save and view them via the
opengl utility moldenogl. Sometimes it results in weird molecules with
unbelievable bonds, but, when it works well, the result is pretty good.

_-_-_-_-_-_-_-_-_-_-_-_-

   Carlos Silva López

Dear Don,

Maybe molden is not a very fancy program, but it is quite a good help
when calculating with gaussian (and it is free!). If you have it, you
can enter the program and use the second button from the top (it looks
like a photographic camera). This command creates one gif file each time
the frame being displayed changes, so just animate the vibration
("normal mode" button) click this button and wait for a while (just
don't forget to click this button again, if you don't want to completely
fill your disk!). Then, you can make an animated .gif with any graphic
program (photoshop...). Another way (smarter) of doing this is to open
molden with the command:

"molden -w 1" and animate the normal mode you want. Then, you open again
with molden the file "freq.dat" that was created in the previous step,
click the camera button and animate the sequence with "movie". Then, you
exit the program and process the *.gif files thus obtained.

Hope it helps.

Regards

Olalla Nieto Faza

Try gOpenMol

http://www.csc.fi/gopenmol/

Jim

Hi Don

I know exactly the problem you're having, I had the same thing myself
last year. I use gOpenMol http://www.csc.fi/gopenmol/ - it isn't the
easiest thing in the world to learn to use, but if you download the
manual (I can't attach it as it is 10Mb) then look at page 203 for the
animation instructions. In fact the whole of app. 5 (starts on page 195)
is what I use all the time. I found that I had to use the stand alone
version of xvibs. If you download it and install it and then can't
figure out how to get it to work then let me know and I'll try to write
out how I do it for animations of vibrations. I guess that you're
wanting to have them in talks - the mpeg is usually under 200kb in size
so it is really good.

Hope this is of help to you

Roma

Hi,

to animate frequencies we use molden. But for recording the video to
play it in presentations we found is useful to use HyperCam (not
HyperChem of course!). This is a general screen-recorder like a screen
capture tool which recorders videos with up to 15 frames per second (I
think). If your machine is fast enough (pentium 600) to animate the
frequencies and record them at the same time you will get a standard avi
file which can be edited with any video editing software.

Regards

Eike Huebner

HyperChem with HyperCam should be able to do this from a checkpoint
file. I think you can save it as an *.avi file to input into PowerPoint.
I did this a couple of years ago with a simple CO2 mode.  The movie is
not 

great quality, but the graphics were acceptable.

James Kubicki

------------------------------------------------------------------------
---------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
[email-masked]
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm