This is a test version of Biostars. For the public version, visit https://www.biostars.org.
PyMol vs DS visualizer for publication images

I need to publish a mutation analysis soon, which will include alignments of pdb files. My only experience is in using PyMol. While this is very practical, I suspect that the exported images aren't that refined.

Is there a preference for using DSvisualizer or other tool when publishing? If so, can anyone direct me to some resources for basic image exportation?

dsvisualizer pymol
• 1,434 views • link
updated by Wayne Wayne • written by Stroodes • Stroodes

1 answer

I read somewhere that PyMol is the most frequently used tool for making images in scientific journals, and I have no problem believing that. Sorry that I can't provide the exact reference, but take a look at journal covers made by PyMol. That is to say that PyMol will work really well unless you have particular aesthetic requirements. Journals for sure will have no problems with high-res images or movies made by PyMol.

In case you want a free alternative:

https://www.rbvi.ucsf.edu/chimerax/

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

This is spot on.
Stroodes, this good, fairly recent introduction entitled 'How to make publication quality images with PyMOL ' stands in stark contrast to the idea expressed in this quote from your post: "While this is very practical, I suspect that the exported images aren't that refined."

More support for PyMOL being popular for publication:

"A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL." - SOURCE: https://proteopedia.org/wiki/index.php/PyMOL

Stroodes, you should explore the ray command, see here for the 'Publication Quality Images' entry at the PyMOL wiki.

• 0 views • link
written by Wayne Wayne

Log in to answer this question.

More posts like this