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I have a collection of pdb files (15), and I want to basically apply the same visualization settings on each one of them and render the image.

enter image description here

I want the above settings, with a certain, resolution and scale for Bonds and VDW. The material is Goodsell for all of them.

It is the same system, just in different configuraitons. All the chemical species present in the system are the same. How do I go about writing a tcl script which applies these to the system and all the atoms? Does anyone have an example where they have played with all of these properties in their tcl scripts?

I would greatly value any advice you have for me!

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    $\begingroup$ There is the possibility to export the current view (and all commands) as a TCL script to further usage. $\endgroup$
    – Camps ♦
    Commented Nov 22, 2022 at 23:31
  • $\begingroup$ Thank you for your response, @Camps. How do I do that? Simply saving visualization state seems to store the information generated for that particular pdb file $\endgroup$
    – megamence
    Commented Nov 22, 2022 at 23:36

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Take a look at the options in the Menu --> File --> Log Tcl Commands to File:

enter image description here

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  • $\begingroup$ Thank you @Camps. However, after I get the file, i save it as x.tcl. Now when I try to source it from vmd, i get errors. Illegal molecule specification '5': Could not find molecule '5'. for example. Is this normal? $\endgroup$
    – megamence
    Commented Nov 22, 2022 at 23:58
  • $\begingroup$ Did you tested with the same molecule that you created the script? $\endgroup$
    – Camps ♦
    Commented Nov 23, 2022 at 13:08

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