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I have a file containing the atomic coordinates (in XYZ format) of a structure, and I also have a list of the partial atomic charges for each atom. I'd like to create an image of the structure where the colors of the atoms correspond to the computed charges. What are some good ways for doing this?

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  • $\begingroup$ (In reply to a deleted comment). I'd be happy if it helps, but I see no benefit in doing so. The XYZ coordinates are a simple $n\times3$ matrix, and the charges are stored as a $n\times1$ vector. The filetype is irrelevant (I can freely convert to any format of your choosing -- CIF, *CAR, XYZ, JMol, etc.). $\endgroup$ – Argon Sep 17 '18 at 22:30
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    $\begingroup$ Alongside the answers below, I found another stackexchange post that is related rather closely, and has a few well discussed options for obtaining your visualization: chemistry.stackexchange.com/questions/76592/… $\endgroup$ – Len_sprague Sep 18 '18 at 3:17
  • $\begingroup$ If you've never heard of IsoDistort you can give it a try. stokes.byu.edu/iso/isodistort.php $\endgroup$ – janst Sep 18 '18 at 3:21
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As far as I know, no software can do this right away but with some work, this should be possible.

Use CYLview to create a povray file, change the atoms to the desired color and render it with Povray. The problem here is that the coordinates of the xyz file and the povray are not the same. But as far as I can tell the numbering stays the same. So if the 3rd atom in your xyz is this:

N       -1.227679000      0.558365000      0.000000000

the 3rd sphere in the povray file would look like that:

sphere {<-1.9762436, 0.9491377, 0.0000000> 0.2812500
   pigment{color rgbt <0.4,0.4,1.0,0.00>}
   finish{F_normal}

All you need to do is change the color here. It should also be pretty easy to automate this color change with some lines of code.

So you can go from this enter image description here

to for example this enter image description here

by simply changing the color value shown above to

pigment{color rgbt <0.2,0.8,1.0,0.00>}
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  • 1
    $\begingroup$ That's an interesting example compound you picked. Personally, I'd rather not go anywhere from it, or from azides in general, except maybe straight away to a safe distance. Preferably taking very careful steps while doing so. But then, I'm not actually a real chemist. :) $\endgroup$ – Ilmari Karonen Sep 18 '18 at 8:42
  • $\begingroup$ @IlmariKaronen that was the first one I found and is straight out of our last project. It's a computational model compound. For experimental work we used the 2-azidoethanol and 2-fluoroethylazide. The former one is no problem to handle, the other one is quite tricky. $\endgroup$ – DSVA Sep 18 '18 at 12:47
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This is easy to do in Avogadro v1.x. For any display type, you can set the color scheme, e.g. through the settings dialog:

enter image description here

Then in the settings window, you pick a color scheme:

enter image description here

Voila, you have a molecule colored by partial charges:

enter image description here

If the file doesn’t come in with partial charges, you can set them via View ⇒ Properties ⇒ Atom Properties:

enter image description here

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It's actually very easy to do this with the free visualization software OVITO (www.ovito.org), where you can color-code atoms according to any particle property you import with your structure (like in your case the partial charges).

Simply import your .xyz file with the partial charges appended as an additional column. During file import you can specify which column contains which information, e.g. positions or charge. Then use the Color Coding modifier and choose "Charge" as "Input Property". Here's the corresponding manual entry: http://www.ovito.org/manual/particles.modifiers.color_coding.html and an example of how that would look like:

Atoms color coded according to partial charges

Hope that helps!

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Have you tried VMD link? It's free, up-to-date, will work with .xyz format files, and would allow you to set charge (or other property) as a color-sensitive characteristic. Here's an example using the bonding coordination (number of nearest neighbors) in a crystal (although only the surface is loaded to conserve memory) enter image description here

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I know you asked for an xyz file, but it is no problem to convert it into a mol2 file. And from there on, you can do this using Chimera.

I take the example molecule from the linked question in the comment section to your question. The corresponding mol2 file would look something like this:

@<TRIPOS>MOLECULE
bla2.xyz
 78 84 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1 N          -0.2152   -3.6116    1.0137 N.2     1  UNL1        -0.980426
      2 N          -0.9072   -3.6634   -1.2690 N.3     1  UNL1        -1.159281
      3 H          -1.0201   -4.5161   -1.2392 H       1  UNL1         0.451727
      4 H           0.5924   -3.5332    3.4084 H       1  UNL1         0.466050
      5 H           1.1383   -4.0685   -6.6623 H       1  UNL1         0.121348
      6 ZN          1.0488    0.3616    1.4618 Zn      1  UNL1         1.085568
      7 C           0.8262    0.8063    4.1826 C.2     1  UNL1         0.885122
      8 C           0.4171    1.4943    5.4556 C.ar    1  UNL1        -0.158259
      9 C          -0.1860    2.7336    5.4577 C.ar    1  UNL1        -0.038223
     10 H          -0.3201    3.1852    4.6583 H       1  UNL1         0.111225
     11 N           3.0298    0.2152    1.0137 N.ar    1  UNL1        -0.989702
     12 N           2.9780    0.9072   -1.2690 N.pl3   1  UNL1        -1.323792
     13 H           2.1252    1.0201   -1.2392 H       1  UNL1         0.552920
     14 H           3.1082   -0.5924    3.4084 H       1  UNL1         0.599787
     15 O           0.6110    1.4120    3.0769 O.3     1  UNL1        -0.805465
     16 O           1.3256   -0.3161    4.2420 O.2     1  UNL1        -0.786727
     17 C          -0.8262   -0.8063   -9.1420 C.2     1  UNL1         0.932072
     18 C          -0.4171   -1.4943   -7.8689 C.ar    1  UNL1        -0.116686
     19 C           0.1860   -2.7336   -7.8668 C.ar    1  UNL1        -0.092391
     20 H           0.3201   -3.1852   -8.6663 H       1  UNL1         0.116237
     21 O          -0.6110   -1.4120  -10.2476 O.co2   1  UNL1        -0.908737
     22 O          -1.3256    0.3161   -9.0825 O.co2   1  UNL1        -0.838830
     23 C          -0.4875   -3.0059   -0.1834 C.3     1  UNL1         1.029873
     24 C           0.2178   -2.5742    1.7916 C.cat   1  UNL1         1.084450
     25 N          -0.2869   -1.7042   -0.1394 N.3     1  UNL1        -0.556339
     26 N           0.1740   -1.4213    1.1643 N.pl3   1  UNL1        -0.669532
     27 H          -1.0626   -3.2357   -1.9987 H       1  UNL1         0.479136
     28 N           0.5884   -2.7456    3.0646 N.pl3   1  UNL1        -1.219932
     29 H           0.8222   -2.0668    3.5390 H       1  UNL1         0.535669
     30 ZN         -1.0488   -0.3616   -1.4618 Zn      1  UNL1         1.115312
     31 C          -0.8262   -0.8063   -4.1826 C.2     1  UNL1         0.930235
     32 C          -0.4171   -1.4943   -5.4556 C.ar    1  UNL1        -0.165126
     33 C           0.1860   -2.7336   -5.4577 C.ar    1  UNL1        -0.068129
     34 H           0.3201   -3.1852   -4.6583 H       1  UNL1         0.125910
     35 C          -3.6355   -0.4875    0.1834 C.ar    1  UNL1         1.112801
     36 C          -4.0672    0.2178   -1.7916 C.ar    1  UNL1         1.089920
     37 N          -4.9372   -0.2869    0.1394 N.ar    1  UNL1        -0.669012
     38 N          -5.2201    0.1740   -1.1643 N.ar    1  UNL1        -0.683650
     39 N          -3.0298   -0.2152   -1.0137 N.ar    1  UNL1        -1.010564
     40 N          -2.9780   -0.9072    1.2690 N.pl3   1  UNL1        -1.379275
     41 H          -3.4057   -1.0626    1.9987 H       1  UNL1         0.465316
     42 H          -2.1252   -1.0201    1.2392 H       1  UNL1         0.591458
     43 N          -3.8958    0.5884   -3.0646 N.pl3   1  UNL1        -1.359821
     44 H          -4.5746    0.8222   -3.5390 H       1  UNL1         0.462374
     45 H          -3.1082    0.5924   -3.4084 H       1  UNL1         0.595021
     46 O          -0.6110   -1.4120   -3.0769 O.3     1  UNL1        -0.846291
     47 O          -1.3256    0.3161   -4.2420 O.2     1  UNL1        -0.789904
     48 C           0.4875    3.0059    0.1834 C.3     1  UNL1         1.054807
     49 C          -0.2178    2.5742   -1.7916 C.cat   1  UNL1         1.079690
     50 N           0.2869    1.7042    0.1394 N.3     1  UNL1        -0.596520
     51 N          -0.1740    1.4213   -1.1643 N.pl3   1  UNL1        -0.651619
     52 N           0.2152    3.6116   -1.0137 N.2     1  UNL1        -0.982105
     53 N           0.9072    3.6634    1.2690 N.3     1  UNL1        -1.153898
     54 H           1.0626    3.2357    1.9987 H       1  UNL1         0.472248
     55 H           1.0201    4.5161    1.2392 H       1  UNL1         0.448303
     56 N          -0.5884    2.7456   -3.0646 N.pl3   1  UNL1        -1.192789
     57 H          -0.8222    2.0668   -3.5390 H       1  UNL1         0.511494
     58 H          -0.5924    3.5332   -3.4084 H       1  UNL1         0.458606
     59 C           0.5990   -3.3114   -6.6623 C.ar    1  UNL1        -0.253677
     60 C          -0.7385   -0.8939   -6.6623 C.ar    1  UNL1        -0.060650
     61 H          -1.1769   -0.0744   -6.6623 H       1  UNL1         0.135692
     62 C           0.8262    0.8063    9.1420 C.2     1  UNL1         0.921571
     63 C           0.4171    1.4943    7.8689 C.ar    1  UNL1        -0.136263
     64 C          -0.1860    2.7336    7.8668 C.ar    1  UNL1        -0.033469
     65 H          -0.3201    3.1852    8.6663 H       1  UNL1         0.092701
     66 O           0.6110    1.4120   10.2477 O.co2   1  UNL1        -0.900753
     67 O           1.3256   -0.3161    9.0825 O.co2   1  UNL1        -0.836472
     68 C          -0.5990    3.3114    6.6623 C.ar    1  UNL1        -0.299314
     69 H          -1.1383    4.0685    6.6623 H       1  UNL1         0.134260
     70 C           0.7385    0.8939    6.6623 C.ar    1  UNL1        -0.048643
     71 H           1.1769    0.0744    6.6623 H       1  UNL1         0.130420
     72 C           3.6355    0.4875   -0.1834 C.ar    1  UNL1         1.071205
     73 C           4.0672   -0.2178    1.7916 C.ar    1  UNL1         1.085316
     74 N           4.9372    0.2869   -0.1394 N.ar    1  UNL1        -0.660949
     75 N           5.2201   -0.1740    1.1643 N.ar    1  UNL1        -0.672967
     76 H           3.4057    1.0626   -1.9987 H       1  UNL1         0.459743
     77 N           3.8958   -0.5884    3.0646 N.pl3   1  UNL1        -1.356568
     78 H           4.5746   -0.8222    3.5390 H       1  UNL1         0.457166
@<TRIPOS>BOND
     1    21    17   ar
     2    17    22   ar
     3    17    18    1
     4    20    19    1
     5    18    19   ar
     6    18    60   ar
     7    19    59   ar
     8     5    59    1
     9    61    60    1
    10    60    32   ar
    11    59    33   ar
    12    33    32   ar
    13    33    34    1
    14    32    31    1
    15    47    31    2
    16    31    46    1
    17    57    56    1
    18    44    43    1
    19    45    43    1
    20    58    56    1
    21    56    49    1
    22    43    36    1
    23    76    12    1
    24    27     2    1
    25    49    51    1
    26    49    52    2
    27    36    38   ar
    28    36    39   ar
    29     2     3    1
    30     2    23    1
    31    12    13    1
    32    12    72    1
    33    38    37   ar
    34    51    50    1
    35    39    35   ar
    36    52    48    1
    37    72    74   ar
    38    72    11   ar
    39    23    25    1
    40    23     1    1
    41    74    75   ar
    42    25    26    1
    43    50    48    1
    44    37    35   ar
    45    35    40    1
    46    48    53    1
    47    11    73   ar
    48     1    24    2
    49    26    24    1
    50    75    73   ar
    51    42    40    1
    52    55    53    1
    53    53    54    1
    54    40    41    1
    55    24    28    1
    56    73    77    1
    57    28     4    1
    58    28    29    1
    59    77    14    1
    60    77    78    1
    61    15     7    1
    62     7    16    2
    63     7     8    1
    64    10     9    1
    65     8     9   ar
    66     8    70   ar
    67     9    68   ar
    68    68    69    1
    69    68    64   ar
    70    70    71    1
    71    70    63   ar
    72    64    63   ar
    73    64    65    1
    74    63    62    1
    75    67    62   ar
    76    62    66   ar

We open it with chimera and then choose Tools > Depiction > Render by Attribute, choose the Attribute to be the charge and click on Apply. This results in a structure that is colored by its partial charges.

partial charge colored molecular structure by chimera

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