Is there a code to convert/visualize a 3d figures (.fig) consisting of chemical bonds and structures into a 2d format, or into .pdb format?

I have some figures of molecules which I want to convert from 3d into 2d for better visualization. I have attached the files for references. In figure 2, the red balls and the charges will remain as it is. Doing them manually is very time consuming and cumbersome. Any help to resolve this problem will be appreciated.

P.S 1.fig is the malab generated .fig file. Figure2.png provides how the structure may appear on visualization post processing.

Answer 1

[Varun]

Hi,

As per my understanding to the question, you want to convert 3d figure (“.fig”) which consists of chemical bonds into 2d image (“.png”) or “.pdb” format.

Please refer the following code to convert 3d figure (“.fig”) to 2d (“.png”) image:

figFile = '1.fig'; 
figHandle = openfig(figFile); 
 
% Set the desired output format and filename 
outputFormat = 'png'; 
outputFilename = 'figure2.png'; 
 
% Save the 2D image 
saveas(figHandle, outputFilename, outputFormat); 
 
% Close the figure 
close(figHandle); 
 
% Read the RGB image 
rgbImage = imread('figure2.png'); 
 
image2D = max(rgbImage,[],3); 
 
% Display the 2D image 
imshow(image2D);

Here is the breakdown of above code:

1. The code opens a MATLAB figure file named "1.fig" and assigns the figure handle to the variable "figHandle".
2. It specifies the desired output format as "png" and sets the output filename as "figure2.png".
3. The "saveas" function is used to save the MATLAB figure as a 2D image in the specified format and filename.
4. The saved image is read using the "imread" function, resulting in an RGB image stored in the variable "rgbImage".
5. The "max" function is applied along the third dimension to convert the RGB image to grayscale. The resulting 2D grayscale image is stored in the variable "image2D".
6. Finally, the "imshow" function is used to display the grayscale image.

As per MATLAB version R2023a, MATLAB does not have any direct “.pdb” conversion functionality.

In order to transform the image into a ".pdb" file, you will require specific software or tools that are specifically designed for converting images into 3D molecular structures like Open Babel or PyMOL.

Hope this helps.