![jmol first glance jmol first glance](https://image.slidesharecdn.com/howarduniversitypresentationver3-101108101741-phpapp01/95/howard-university-presentation-ver3-19-638.jpg)
This study has focused on freeware since neither students nor faculty are usually willing (or able) to pay for commercial molecular visualization software when freeware applications are available.
#Jmol first glance free#
Although a version of PyMOL is free for educational use, it requires licensing and is unsupported by the company. Arguably, the molecular visualization application, which produces the highest quality images and movies, is PyMOL, written in the versatile Python language by Warren DeLano ( PyMOL is now distributed as a commercial product by Schrödinger. Two particularly powerful stand-alone applications are DeepView (aka Swiss-PDBviewer), developed by Nicolas Guex as an interface to the SWISS-MODEL automated homology modeling server, and Chimera, which was developed by UCSF researchers with support from NIH. A well known example is Cn3D, which was developed as the structure visualization tool for the NCBI Entrez database. In addition to the above structure visualization software, other freeware standalone applications were developed either as structure-based interfaces with databases or server applications. The latter is used as a structure viewer for the PDB both directly at the PDB and through independent sites, which access the PDB including FirstGlance ( ), Protein Explorer ( ), and Proteopedia ( ). Chime eventually was replaced by the Java-based, open source program Jmol, which can be run as a standalone application or a web browser applet. Web pages containing Chime-viewable structures became very popular in biochemistry education because of the ease of use by the student and the retention of scripting commands from RasMol. The first of these was the Chime browser plug-in distributed freely by MDL. With the advancement of personal computing and the Internet came migration of elements of RasMol to web-based programs. Since that time, educators have used both programs while Kinemage and RasMol themselves have continued development. Shortly afterwards, Roger Sayle introduced RasMol, which could read PDB files directly. The original freeware program MAGE, written by David Richardson, was used to display kinemages, plain text files derived from the Protein Data Bank (PDB) coordinate files associated with articles published in Protein Science. Since the introduction of molecular graphics freeware for use in structural biology in the early 1990's, biochemistry educators have used them in diverse ways in an effort to enhance the student learning experience. This quotation from a participant in our study nicely illustrates the enjoyment that many biochemical educators feel that the tools of molecular visualization have brought to the learning environment, both for instructor and student. I think molecular visualization has fueled my love of teaching biochemistry.” When I had biochemistry as an undergraduate, it was black ink on an overhead projector. “I can't imagine teaching biochemistry without molecular visualization. While a minority of instructors used a grading rubric/scoring matrix for assessment of student learning with molecular visualization, many expressed a desire for common use assessment tools. The most common uses of molecular visualization in teaching were lecture and lab illustrations, followed by exam questions, in-class or in-laboratory exercises, and student projects, which frequently included presentations. The majority of respondents had used molecular visualization for more than 5 years and mentioned 32 different visualization tools used, with Jmol and PyMOL clearly standing out as the most frequently used programs at the present time. Many common themes arose in the survey and the interviews: a shared passion for the use of molecular visualization in teaching, broad diversity in software preference, the lack of uniform standards for assessment, a desire for more quality resources, and the challenge of enabling students to incorporate visualization in their learning. To provide more depth to these results, interviews were conducted with 12 of the participants. Participants ( n = 116) were asked to complete 11 multiple choice and 3 open ended questions. We have conducted a survey to begin a systematic evaluation of the current classroom usage of molecular visualization. It is a compelling medium that can be used to communicate structural information much more effectively with interactive animations than with static figures.
![jmol first glance jmol first glance](http://www.jle.com/e-docs/00/04/5B/2C/texte_alt_jlevir00379_gr4.jpg)
As biochemists, one of our most captivating teaching tools is the use of molecular visualization.