Comments on: What is your favorite molecular viewer ?

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 [...]

By: Xavier Ambroggio

Xavier Ambroggio — Mon, 06 Apr 2009 10:46:26 +0000

The percentages reported by the poll are a little strange. They round to the nearest integer (even through they report the tenths decimal place) and they round down. So… 0.9% would be reported as 0.0%. The order is correct, meaning that MOLDEN ranking above DSVisualizer means that either MOLDEN has more votes or is tied with DSVisualizer.

By: Moshe Goldstein

Moshe Goldstein — Sun, 29 Mar 2009 06:23:05 +0000

When I need only visualization, I prefer most of the time to use Raswin because of the following: (a) it is very easy to learn how to use it; (b) it is very intuitive; (c) its graphics are of enough good publishable quality;(d) from the moment you learned its simple but powerful command line language, it is very easy to right scripts for it – though I would like it to have more powerful programming capabilities.
I should say that there are more powerful viewers, but the compactness and ease of use of Raswin are its strength and beauty.

Moshe Goldstein, PhD candidate
The Hebrew University of Jerusalem

By: Vasiliy Znamenskiy

Vasiliy Znamenskiy — Tue, 24 Mar 2009 11:43:18 +0000

I use GaussView, gOpenMol, VEGA ZZ.

By: Giuseppe Stavole

Giuseppe Stavole — Sun, 22 Mar 2009 21:35:22 +0000

Jmol is very simple to use and very fast to learn.
It is written in java so is highly portable.
Both at school where linux used and at home where pupils still use windows.
Pupils’s favourite feature: 3d molecules in anamorphic.

Giuseppe Stavole
high school chemistry teacher
Bolzano Italy

By: Wes

Wes — Sun, 22 Mar 2009 18:10:42 +0000

I like BALLView myself. It has Python scripting, sophisticated rendering, and the learning curve seems shallower than PyMOL’s.