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Use Molden to view orbitals (Read 9747 times)
Gerrit-Jan Linker
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Use Molden to view orbitals
21.08.08 at 10:41:51
 
Use Molden to view orbitals
 
The molden program can be used to view orbitals calculated with the MOLCAS package. The project.scf.molden.autosaved file can be read into MOLDEN for viewing.
 
First an X terminal must be started and the xhost + command must  be issued.
Then on the unix shell the display environment variable  should be set to send the output to the xwindows environment:
export DISPLAY=machine:0.0
Replace machine with the name or ip address of the system where the x terminal has been started.
 
In the unix shell start molden by just typing: molden.
 
The MOLDEN front-end opens. Use the read button to read in the above mentioned file.  
 
To view your structure in ball stick mode click the solid button and select ball stick.
 
To view the orbitals, press the dens. mode button. Note that you can switch back using the mol. mode button.
 
In density mode you can select an orbital or press the homo or lumo button to select an orbital. The space button can be used to set the density for which you want to see the shape. Enter e.g. a density of 0.05.
 
If you don't like the display of the molecule in dens mode, switch back to molecule mode and you will see that the shapes of the orbitals are still visible.
 
To save the images you view as gif files, first switch back to molecule view. Press the camera button. Then switch back to density mode to view the orbitals. Each time molden shows a new image a copy will be saved as a .gif.
 
See also:
Molden home page
http://www.cmbi.ru.nl/molden/molden.html
Using MOLDEN in windows on a PC
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1207465443
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« Last Edit: 21.08.08 at 12:08:13 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
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Gerrit-Jan Linker
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Re: Use Molden to view orbitals
Reply #1 - 18.09.08 at 11:15:49
 
Plotting molcas orbitals with gabedit
 
To get higher quality images the gabedit software can be used to view molden output files that contain orbitals.  
 
Example:

 
Reference:
http://gabedit.sourceforge.net/
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« Last Edit: 18.09.08 at 12:16:41 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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Re: Use Molden to view orbitals
Reply #2 - 17.08.09 at 15:51:35
 
You can also use the molcas grid viewer. See
 
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1250434008
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Gerrit-Jan Linker
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Molden: create povray output
Reply #3 - 04.04.14 at 14:54:34
 
Molden: create povray output
 
With molden a povray file can be created to make high quality orbital plots using the povray raytracing software. In order to create the povray file select the icon with a "V and an R" (excuse the vague description) and select povray. Enter a file and iso value (0.04 e.g.). Use the povray software to render this file to a png output file:
povray myfile.pov
 
To control the size of the created png file you can use the -Wx and -Yx switches:
povray -W1000 -Y1000 myfile.pov
 
The .pov file can be edited.  
 
To give a zoomed out image you can e.g. change the camera location
camera {
 location <0.0, 0.0, 5.0>
 
For a white background, add this line:
 background { color rgb<1,1,1> }
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« Last Edit: 01.12.16 at 16:57:42 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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