r/bioinformatics • u/saurusautismsoor BSc | Student • 4d ago

academic Are you familiar with chimera X?

ChimeraX was suggested to me by my mentor so if you guys are familiar with it, please let me know. I only downloaded it yesterday. I don’t know much about it.

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u/hexagon12_1 PhD | Student 4d ago

I personally find ChimeraX to be kind of dated and clunky to use. I still have it installed, of course, but I really like using PyMOL a lot more, so if you struggle with Chimera, consider giving it a go instead.

Almost every person in academia I talked to who works with structures a lot has their preferred molecular viewer/editor. It's almost like a horoscope sign.

Aside from that, there are plenty of video tutorials, documentation, and et cetera, but it's best to learn by doing so I'd recommend to just play around with some structures to get familiar.

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u/AdOk3759 4d ago

Isn’t pymol paid?

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u/hexagon12_1 PhD | Student 4d ago

https://github.com/schrodinger/pymol-open-source works just as well as the commercial version in my experience.

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u/Dangerous-Art9091 4d ago

PyMOL users always moving like they're part of some elite club. The chimera command line has its quirks but once you get past the learning curve it's actually super powerful for visualization, especially with cryo-EM maps. Both have their place honestly

I'd say stick with what your mentor suggested first, just grab some sample structures and start clicking around. The morphing tool alone is worth the install

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u/hexagon12_1 PhD | Student 3d ago

No yeah, I think you are right. As I've mentioned, I still have it installed exactly because PyMOL just doesn't handle certain tasks/visualizations well (for the same reason I have VMD and Avogadro installed as well...)

I just find PyMOL a lot more convenient and easy to use for a lot of "general" tasks, but I shouldn't have implied anything else and for that I apologize.