Comments on: What is your favorite molecular viewer ?

By: Anne

Anne — Tue, 30 Aug 2011 22:43:00 +0000

I use MOE – excellent, and beautiful (includes POV ray rendering).

On the free side I of course love VMD, and QuteMol

By: Use of Molecular Vision in Education | Macromolecular Modeling Blog ™

Use of Molecular Vision in Education | Macromolecular Modeling Blog ™ — Sat, 09 Oct 2010 15:11:37 +0000

[...] while you’re at it, you might want to revisit our poll on your favourite macromolecular viewer. Share [...]

By: Matthieu Montes

Matthieu Montes — Thu, 23 Sep 2010 14:49:11 +0000

I used PyMol and ICM for research and used to teach using PyMol. I will change for another program since Pymol is not free and opensource anymore since schrodinger took over the licensing.

Thus I will switch back to VMD.

By: Dale Schruben

Dale Schruben — Tue, 06 Apr 2010 15:51:37 +0000

how did the poll come out?

By: Joost Van Durme

Joost Van Durme — Wed, 24 Mar 2010 08:53:39 +0000

I used PyMol, VMD, RasMol and YASARA, and stayed with YASARA for years now.
YASARA is extremely fast whilst displaying the coolest 3D graphics around. The different scenes (viewing styles) are adaptable with 1 button and give me an instant clarity on sidechains, fold, etc …
I also added my own menus and commands to YASARA with customizable options by just writing simple (or more complex) plugins in Python.
Love it!

By: Vincent LG.

Vincent LG. — Fri, 18 Dec 2009 13:52:42 +0000

I usually use Pymol or VMD. VMD has great rendering capabilities, while pymol is a bit more user friendly.

Note that OpenAstex is a very nice alternative, especially for web pages (as an applet). It has a powerfull scripting language, similar to that of Jmol but much more easy to use in my opinion.

By: Iain

Iain — Wed, 24 Jun 2009 12:32:07 +0000

I’ve always used VMD, but I have to admit I’m a little dissapointed with its ability to superimpose structures that don’t have a 1-to-1 residue match.

There is one package, called Quanta, which doesn’t appear on the list and doesn’t seem to be very popular. Its a great little tool for manipulating structures – changing rotomers and backbone conformations is easy and manual. It is easy to insert or remove residues, with algorithms to clean up the structure afterwards, plus it interfaced with CHARMM nicely.

By: Serge

Serge — Fri, 19 Jun 2009 12:06:25 +0000

The choice of a viewer or modeler is a difficult question. The answer depends on what sort of a user we have. As I saw one day, a chemist studying protein-ligand docking / steric restrictions was delighted by the not too well known PV protein modeler. On the other hand, PyMOL could be the best choice for presentations.

By: MK

MK — Thu, 18 Jun 2009 15:52:47 +0000

I voted for Pymol but I use MOLMOL just as frequently. Visualizing a bundle of NMR structures, MOLMOL is easier. What’s happened to MOLMOL? Nobody uses it anymore?

By: What is your favorite journal in the field of computational structural biology? | Macromolecular Modeling Blog ™

Thu, 23 Apr 2009 18:56:50 +0000

[...] the success of our previous poll which was followed by an extensive and interesting discussion, and in order to better our [...]