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I'm trying to color certain amino acid's van der waals bonds as in the following picture:

enter image description here

can anybody please describe the steps to accomplish that?

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Use Photoshop? Please clarify, I assume you want to do this using the same program that produced the image, so tell us what you're using! –  terdon May 13 at 14:53
    
If I'm right in assuming you are trying to get colouring like the purple AA VDW bonds then I can only specifically colour VDW bonds in solid 3D view (under display, Render in solid 3D) in SPDBV but not when solid 3D view is not activated, as in the example in your picture. One option is to use POV-Ray but I haven't worked with it. –  Bez May 14 at 1:10
    
@Bez thank you, so I guess it's possible only via 3d mode, please consider writing your comment as an answer so I could mark it as the right one –  Ranco May 15 at 11:01

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If I'm right in assuming you are trying to get colouring like the purple AA VDW bonds then I can only specifically colour VDW bonds in solid 3D view (under display, Render in solid 3D) in SPDBV but not when solid 3D view is not activated, as in the example in your picture. One option is to use POV-Ray but I haven't worked with it.

If the purple colouring is not photoshoped by the authors of the paper you got the picture from, then the chances are they have written a custom script for it in the software, which allows them to do this. So I would just contact the corresponding author and ask them how they managed it and if they have done it through a script or some other software. Most of the time people are happy to share their methodology once they have published it!

Also have you tried the Jalview software? Although it's designed primarily as an alignment tool but it has a nice 3D Jmol view. You can load up your sequence and the associated PDB file and you can play around with it. The graphics output are quite publication friendly. I'm not an expert at it and I've only been playing around with it for a bit but when you get the hang of it, it's quite nice graphically. Although the VDW view is still space fill 3D but it's a bit nicer as it has opacity etc etc. Just download it and as soon as you open it up, you are presented with an example alignment and Jmol view. Just play around with the alignment section and the Jmol view and see if you like the aesthetics. The only tricky part in the software is getting the residues you want selected but once you manage that, you can get the program to display VDW only for the selected residues.

Hope this helps.

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You might also want to look at which version of SPDBV was used to generate that image. It's not uncommon that certain features of applications get disabled in new versions for whatever reason. –  Bez May 17 at 16:05

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