Command line rendering of chemical structures in Blender

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in preparation, absolute beginner friendly: Here is a procedure on how to take a CONTCAR and convert it to high quality PNG image.

Installing Blender

• Blender is installed by downloading the code (https://www.blender.org/download/) unpacking it to a path of your choosing.
• In the program folder you will find an executable called blender

example: /usr/bin/blender-2.80-linux-glibc217-x86_64

• To launch blender you will execute (if you use the path from previous line)

/usr/bin/blender-2.80-linux-glibc217-x86_64/blender

• you do not need to launch blender at this point

Preparing the structure

I am assuming that you are more or less familiar with the use of vtst-scripts (http://theory.cm.utexas.edu/vtsttools/scripts.html), openbabel (http://openbabel.org/wiki/Main_Page) or just check out Scripts for VASP

• Let's start from the same spot, do this:

$ mkdir ~/blender_test
$ cd ~/blender_test

move the CONTCAR you want to render to ~/blender_test

$ ls
CONTCAR

• Let's render HCl molecule for example:

$ cat CONTCAR
HCl                          
1.0
10.0000000000 10.0000000000 10.0000000000 
10.0000000000 10.0000000000 10.0000000000 
10.0000000000 10.0000000000 10.0000000000  
 H Cl
 1 1
Selective
Cartesian
 +0.0000000000  +0.0000000000  +0.0000000000  T T T
 +1.0000000000  +0.0000000000  +0.0000000000  T T T

• if you do use openbabel:

$babel CONTCAR hcl.pdb
$cat hcl.pdb
COMPND    HCl 
AUTHOR    GENERATED BY OPEN BABEL 2.4.1
CRYST1   17.321   17.321   17.321   0.03   0.03   0.03 P 1         1
HETATM    1  H   UNL     1       0.000   0.000   0.000  1.00  0.00           H  
HETATM    2 CL   UNL     1       1.000   0.000   0.000  1.00  0.00          Cl  
CONECT    1    2                                                      
CONECT    2    1                                                      
MASTER        0    0    0    0    0    0    0    0    2    0    2    0
END

• so now you have:

$

MISC NOTES

Notice the two lines of hcl.pdb starting with "CONECT", those are important to draw bonds in blender. Not all converters include bonds in the output pdb file. Good news is that this also works:

COMPND    HCl 
AUTHOR    GENERATED BY OPEN BABEL 2.4.1
CRYST1   17.321   17.321   17.321   0.03   0.03   0.03 P 1         1
ATOM      1  H   UNK     1       0.000   0.000   0.000  1.00  0.00           H  
HETATM    2 CL   UNL     2       3.000   0.000   0.000  1.00  0.00          Cl  
MASTER        0    0    0    0    0    0    0    0    2    0    2    0
END

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