PDB visualization methods

Question

[juara]

Hello

I would appreciate if you guys can help me. I am very new in proteomics world. I am looking for a way to better visualize PDB files. I understand there are programs in addition to what pdb website offers, but I was not able to find a way to what I would like to achieve. Specifically, I am looking for a way to visualize the protein structure and the ligand (Histone modifications, as an example) bound to it. Kinda like what is published in figure 4 of this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130114/

I would really appreciate your help.

Answer 1

[t_stranger]

1. UCSF Chimera
2. DS Visualizer

Both softwares are free and able to visualize the pdb file format

[juara]

Thanks. DS Visualizer does not support mac. Chimera has very basic features unless I do not know how to use it. Is there a way in Chimera to just display one side chain/atom? How can I eg display only Zn ions and not all other atoms? Thanks for your help in advance.

[t_stranger]

select the Zn ion ( ctrl + click the Zn ), invert the selection, hide the selection under action tab. Or u can select the residue under select tab.

It can either run in command or graphic. If u prefer command, you can try to use it. Open the command line under Favourite tab

[Joe]

Chimera is my favourite, followed by PyMOL which others have mentioned:

Chimera has very basic features unless I do not know how to use it.

You don't know how to use it. Chimera has more visualisation tricks and tools than any other tool I've found. Not to mention by far the most extensive documentation, tutorials and a dedicated help forum that the developers themselves answer.

[juara]

Thanks for the input. I will look at it more closer instead of jumping from one tool to the other

Answer 2

[Alex Reynolds]

PyMOL

[juara]

Thanks for your suggestion. Is there a free trial for PyMOL?

[Alex Reynolds]

I've no idea. I think there's a free version for academia, if you qualify for that.

[Joe]

Yes, there's an education version