What is your favorite molecular viewer ?

One of the main tools of the structural biologist (computational or experimental) if not, THE main tool, is the molecular viewer he uses. There are various viewers available, but usually each of us, at a certain point at his career, chooses a specific one and specializes in it. It becomes a way of self expression, to the point that using a “non-native” viewer is like talking in a foreign language. (How do I select only the polar atoms within 4.5A of chain B and color them CPK in this awkward viewer ?!?!?! On MY viewer it would take me a second!)

We want to hear what is YOUR molecular viewer of choice. Each viewer is optimized for a different set of tasks. E.g. VMD is designed for molecular dynamics, UCSF Chimera integrates many molecular analysis tools, Rasmol is a quick and dirty command line operated little fellow, not producing the nicest figures though, PyMOL creates good looking figures and is highly scriptable (as we demonstrated before in PyMOL scripts), while Jmol is web oriented and easy to embed in web pages.

What is your favorite molecular viewer ?

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There are other software available, please tell us in the comments what’s your favorite viewer advantages and what are the disadvantages of the other “lesser” 😉 viewers.

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  • Xavier Ambroggio

    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.

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  • MK

    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?

  • Serge

    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.

  • Iain

    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.

  • Vincent LG.

    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.

  • Joost Van Durme

    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!

  • Dale Schruben

    how did the poll come out?

  • Matthieu Montes

    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.

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  • Anne

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

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

  • rjrich

    Recently, I have been using YASARA-Structure as my default, but I am also taking a serious look at MOE to use in parallel. On the free side, I like UCSF Chimera and PyMOL. VMD is packed with features, but its interface and ease of use need to be improved.

  • Osvaldo Martin

    PyMOL is open source and the sourcecode is freely available (you only have to paid for precompiled binaries)

  • Nikitin Alexey
  • ???????

    I was using PyMol and VMD for a long time, but since I’ve introduced myself to BallView – like it most.

  • rjrich

    Chem3D (Perkin-Elmer/CambridgeSoft) is an excellent viewer and molecular modeling platform that provides a GUI for Conflex, Gamess, Gaussian, MOPAC, and Autodock.

  • Mukesh Raj

    I am new to the field of bioinformatics and trying to dock antigen-antibody in patchdock. Antigen crystal structure is known and I am using the .pdb file of it whereas antibody has been modeled by Itasser. The docked model shows only one sequence which contains residues of both (antigen as well as antibody) arbitrarily when opened in PyMol.
    I am not able to mark the two molecules.
    Please suggest.

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