A survey of educational uses of molecular visualization freeware


Address for correspondence to: Rochester Institute of Technology, School of Chemistry and Materials Science, Rochester, New York 14623, USA. E-mail: pac8612@rit.edu


As biochemists, one of our most captivating teaching tools is the use 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. We have conducted a survey to begin a systematic evaluation of the current classroom usage of molecular visualization. Participants (n = 116) were asked to complete 11 multiple choice and 3 open ended questions. To provide more depth to these results, interviews were conducted with 12 of the participants. 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. 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. 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. 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. © 2013 by The International Union of Biochemistry and Molecular Biology, 41(3):193–205, 2013


  • “I can't imagine teaching biochemistry without molecular visualization. When I had biochemistry as an undergraduate, it was black ink on an overhead projector. I think molecular visualization has fueled my love of teaching biochemistry.”

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. 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. 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 [1-3]. Shortly afterwards, Roger Sayle introduced RasMol, which could read PDB files directly [4, 5]. Since that time, educators have used both programs [6] while Kinemage and RasMol themselves have continued development [7, 8]. With the advancement of personal computing and the Internet came migration of elements of RasMol to web-based programs. The first of these was the Chime browser plug-in distributed freely by MDL. 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 [9-11]. Chime eventually was replaced by the Java-based, open source program Jmol [12-15], which can be run as a standalone application or a web browser applet. 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 (firstglance.jmol.org), Protein Explorer (jmol.proteinexplorer.org), and Proteopedia (proteopedia.org).

In addition to the above structure visualization software, other freeware standalone applications were developed either as structure-based interfaces with databases or server applications. A well known example is Cn3D, which was developed as the structure visualization tool for the NCBI Entrez database [16-18]. Two particularly powerful standalone applications are DeepView (aka Swiss-PDBviewer), developed by Nicolas Guex as an interface to the SWISS-MODEL automated homology modeling server [19], and Chimera, which was developed by UCSF researchers with support from NIH [20, 21]. Arguably, the molecular visualization application, which produces the highest quality images and movies, is PyMOL, written in the versatile Python language by Warren DeLano (www.pymol.org). PyMOL is now distributed as a commercial product by Schrödinger. Although a version of PyMOL is free for educational use, it requires licensing and is unsupported by the company.

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. Since most of the above mentioned applications are open source and readily adaptable to database mining and research-level structure exploration, they have been maintained largely by the structural biology research community. This rich variety of applications freely available for educational use has been a boon to biochemistry educators from the start, and molecular visualization exercises and/or animations are now routinely distributed with biochemistry textbooks. Some faculty such as Angel Herráez, Eric Martz and Gale Rhodes, have even focused their scholarly activities on biochemistry education with molecular visualization [22-24]. The field has matured to the point that we felt it would be useful to document current practices through a community survey followed by interviews with selected practitioners (the source of the opening quote). The specific research questions are listed below.

  1. What is the profile of the typical instructor who uses molecular visualization in terms of faculty rank and experience with visualization tools?
  2. Which molecular visualization tools are currently preferred by the biochemistry education community?
  3. How are these tools incorporated into their pedagogical approaches?
  4. What forms of assessment of student learning are commonly used when teaching with molecular visualization?
  5. What software enhancements and other molecular visualization teaching resources would the biochemistry education community like to see developed and available for use?


A survey (Appendix A) consisting of 14 questions was prepared and posted on Survey Monkey (www.surveymonkey.com), following review by three chemistry or biochemistry education specialists. Invitations to participate in the survey were sent as letters to the editors of “Biochemistry and Molecular Biology Education” [25] and “ASBMB Today” [26]; the invitation was also posted to the following listservers: molvis-list@bioinformatics.org, pdb-l@sdsc.edu, proteopedialist-for-users@bioinformatics.org, rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net. Surveys were conducted anonymously. We received 116 completed surveys.

To characterize the survey participants, we began the survey with five demographic questions (only one answer allowed) about the respondents’ academic rank, operating system preference, and history and frequency of teaching use of molecular visualization. The final demographic question allowed respondents to select one or more courses in which they have used molecular visualization. We then provided a list of free molecular visualization programs and asked respondents to indicate the program(s) they formerly and presently use, to look for clear preferences in the user community. For this question and all subsequent questions, a comment box was included to collect open-ended responses in case the available choices were not sufficient.

The next three questions addressed pedagogy. First, respondents were asked how they use molecular visualization in teaching and were allowed to select any or all of the nine choices provided, ranging from demonstration only to required online resources. The second question focused on assessment of learning using molecular visualization, with options ranging from no grading to weighted grading rubrics. Those with rubrics were asked to submit them to the authors. The third question asked if students were ever required to create molecular visualization resources for classes.

Two questions about practice followed. The first focused on user satisfaction with a number of popular molecular visualization programs, with options ranging from “extremely satisfied” to “disgruntled and ready to go postal.” Next, we asked how users obtained resources for classroom use.

The survey concluded with three open-ended questions about (a) additional resources they would like to see, (b) additional features they would like to have available in the programs they use, and (c) any other questions or comments they would like to make.

The first draft of the survey was created by the authors. It was subsequently refined by a colleague with a Ph.D. in Chemical Education who was familiar with survey design. Finally, we circulated it to a number of well-known practitioners in the molecular visualization community. Their comments and suggestions were incorporated, with a particular focus on minimizing ambiguity in the questions and the answers (Appendix A).

To add further depth to our study, we conducted individual 30 min interviews with 12 people who are active in the molecular visualization community using ooVoo (www.ooVoo.com), which enabled us to video record the interviews. These people were invited based on articles they had contributed to “Biochemistry and Molecular Biology Education,” active participation in molecular visualization listservs, or self-identification in emails they submitted to the authors after completing the online survey. Before beginning, the interviewees were asked to grant informed consent (Appendix B). The quotes in the paper are extracted verbatim from comments included in the survey or from transcriptions of the interviews. The interview consisted of several questions (Appendix B) that had been taken from the survey, plus additional questions that were designed to delve more deeply into the backgrounds of the interviewees, as well as their practices. They were asked to describe and classify their institutions, then to define their primary field of study. We asked them to provide a detailed history of their “journey in using molecular visualization,” including questions on their personal preference for software. Next, we asked about their pedagogical approach, with questions about student projects, the use of physical models, and the forms of assessment they use in their classes. We then discussed their use of molecular visualization in assessment at three levels: (a) was molecular visualization included in any of their normal assessment tools (exams, homeworks, etc.)?, (b) do they have rubrics that contain molecular visualization?, and (c) have they developed rubrics for directly assessing student learning when the students use the molecular visualization themselves? The survey and interview documents, which include an informed consent statement and questions, are available as Supporting Information.

The survey and interview questions and procedures were reviewed and approved by the RIT Human Subjects Research Office (Federal Wide Assurance# FWA00000731). Survey participants were required to electronically sign an informed consent before proceeding with the survey.

Survey Results


The first few questions of the survey focused on demographics. Survey respondents included graduate students (13%), postdoctoral fellows (11%), lecturer (14%), assistant professors (16%), associate professors (27%), and full professors (21%)1. Experience with molecular visualization ranged from >5 years (30%), 5–10 years (33%), 10–15 years (25%) to >15 years (12%). Windows (all versions, 70%) was the most popular operating system, followed by Macintosh OS X (32%) and Linux (29%); respondents were allowed to select more than one answer for this question. Frequency of use ranged from >10 times per year (56%) to 5–10 times per year (21%) to 1–4 times per year (22%). Molecular visualization was used most frequently in biochemistry courses (62%), followed by cell biology (39%), molecular biology (16%), organic chemistry (12%), pharmacology (4%), and general biology (3%).

User Preferences

One of our most interesting questions was about preference in molecular visualization software. Multiple programs (Jmol, RasMol/RasTop, PyMOL, Chimera, Molmol, CN3D, DeepView, Kinemage/KING, Protein Explorer, Proteopedia.org, FirstGlance in Jmol, RCSB PDB Protein Workshop) could be selected. Users indicated whether they had used a program in the past and whether they currently use a program, either sometimes or usually. Comments were also allowed. The results in Fig. 1 reflect use for the three most popular programs: RasMol, Jmol, and PyMOL, with all other choices grouped under “Other” and listed by frequency in the figure legend.

Figure 1.

Preferences for Molecular Visualization Software. The question, “Which molecular visualization program(s) do you use?” could be answered with multiple selections: used in the past, used sometimes or usually used. Jmol (all forms) refers to any program or website based on Jmol including Jmol (freestanding), Protein Explorer, FirstGlance in Jmol, and Proteopedia.org. Responses grouped under “other” included Chimera (12–past, 11–sometimes, and 6–usually), MolMol (7, 4, and 0), CN3D (13, 4, and 1), DeepView (18, 16, and 6), Kinemage/KING (13, 10, and 2), and RCSB PDB Protein Workshop (7, 12, and 2). Under comments, users added VMD (9), COOT (7), Chime (6), YASARA (5), Molsoft ICM (5), Avogadro (3), GaussView (2), Spartan (2), Discovery Studio Visualizer (2), AutoDock (1), BRUGEL (1), CCP4mg (1), Chemcraft (1), DS Visualizer (1), iMol (1), Jena3D Viewer (1), Maestro (1), MOE (1), MoG (1), Molecular Workbench (1), Molekel (1), Molscript/Render3D (1), and VIDA (1). Numbers in parentheses indicate the number of responses in each case.

We also probed user satisfaction with this question: “How happy are you with the visualization program you are currently using?” (one program could be selected for each level of satisfaction; comment option available). Most (64 of 93) respondents were extremely satisfied, with Jmol (18) and PyMOL (20) being the most frequent choices. Only 20 respondents were dissatisfied or worse, with no programs receiving more than three responses in this category.

Pedagogical Approaches

People reported using molecular visualization in a variety of settings (Fig. 2), with 90% indicating that they use it for demonstrations in lecture and laboratory. Responses about assessment were explored further with additional questions in both the survey and the interviews.

Figure 2.

Educational Uses of Molecular Visualization. Respondents to the question, “How do you use 3D molecular visualization?” were allowed to select as many of the 9 options as applied to their usage. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]


The multiple choice question, “Have you attempted to assess molecular visualization in your courses?” (multiple answers allowed; comment option available), yielded these results: 43 of 74 respondents answered no; 16 responded that they grade it conversationally to see if the students understood what they did; 22 stated that they use a formal grading rubric that counts between 2 and 10% of the course grade. We also inquired about student creation of 3D molecular visualization resources. Half of the 94 respondents had a required class exercise, 42 had students create molecular visualizations as part of their research group, and 15 had students use molecular visualization to create either websites or Proteopedia [27] pages.

Teaching Resources and Software Enhancements

With our last multiple choice question, “How do you obtain molecular visualization resources for your classes?” we found that most users (75%) created their own materials. The second and third most popular choices were the PDB (61%) and Google (25%).

The survey concluded with three open-ended questions that are listed here with a summary of responses. The first question asked about additional resources they would like to have available to teach molecular structures. Some of the answers (32 total responses) related to facilities (more computer laboratories or software licenses). Others requested enhancements to the software (Jmol on the iPad, molecular interactions software, a 3D molecular model builder on a web page, molecular dynamics calculations in freeware). One frequent request was for a centralized online resource containing tutorials, quizzes, and homework assignments that can be readily shared with others.

The second open ended question asked about capabilities in 3D molecular visualization that are not currently available. The most common request was for a simple way to create animations/morphs between structures (7 of 41 responses), followed by a desire to do sequence and/or structure alignments within the software (4 of 41) and the ability to mutate amino acids in a structure (3 of 41). It should be noted that some of these features are available in Jmol (3D molecular model builder, and molecular dynamics calculations), PyMOL (structure alignments), and DeepView (mutation of amino acids in a structure, http://tinyurl.com/aamutation). In addition, the Yale Morph Server provides users with tools for morphing between two structures [28].

In the final open ended question, respondents were asked if they had any additional questions or comments that had not been included in the survey. There were several requests for tutorials or help files, particularly relating to more advanced features such as docking scores with ICM-Pro or the ability to investigate specificity of a family of proteases in a single screen. There were several requests for better help files and for better instructions on converting Chime pages to Jmol pages. Several people talked about student perception and student learning, in light of what is known about visual learners and misconceptions that are often drawn from static images or the general perception that structural learning is difficult or inaccessible [see e.g., 29–31]. There were also comments about developing rubrics for structural learning and about comparing the results from this survey, directed at a more biological/biochemical audience, with a similar survey that could be targeted for a more chemical audience. There was general support for carrying this project forward to build the community of educational users of molecular visualization.

Interview Results

Demographics and User Preferences

To further our investigation into the uses of molecular visualization in the classroom, we engaged in a set of interviews. The interviewees ranged in rank, although the majority of the interviewees were tenured, full professors. A variety of institutions were represented, from comprehensive universities to research universities to primarily undergraduate institutions. All interviewees used molecular visualization in the classroom and most used it in their research, as well. Likely due to our selection of the pool of interviewees, all of the scientists agreed that molecular visualization was an effective tool for teaching and all made great efforts to include it as part of their standard curriculum. As seen in the survey results, the interviewees’ choice of molecular visualization resources varied greatly, although RasMol, Jmol, and PyMOL were mentioned the most. Although the interviewees were asked many of the same questions from the survey, the interview process allowed for more in-depth answers and discussion, most of which focused on the use of molecular visualization in the classroom and student assessment.

Pedagogical Approaches

While many of the interviewees used molecular visualization in short activities and during demonstrations, the most popular use of molecular visualization in the classroom was in the form of student projects. In addition to just “looking” at the molecules, most of the interviewees used molecular visualization as a tool to show students the structure-function relationship: “Being able to show structures and manipulate them …. It all comes down to structure yields function. Without molecular visualization, I think it's hard to make that point a lot of times. Visualization has really changed the way we can teach biochemistry, the way students can learn biochemistry.”

Many of the interviewees were able to incorporate molecular visualization into their teaching in creative and innovative ways. Several interviewees allowed students to work in groups, which often enhanced the learning process. One interviewee introduced molecular visualization as a useful tool for students interested in elementary education and also used it to visualize a geological crystal series. Some of the interviewees mentioned the use of molecular visualization as part of their hands-on learning curriculum, replacing in-class lectures with online or video lectures and allowing class time to do hands-on activities and experiments. Physical models were also popular among many of the interviewees: “Physical models are sort of making a comeback. They are so powerful for comparing the relative sizes of things.” Many used 3D printing models and other physical interpretations of macromolecules to help students understand challenging concepts such as relative sizing of proteins and other significant biological entities (such as viruses or bacterial cells), ligand docking, and protein-protein interactions. The use of molecular visualization in combination with physical models allows for a multimodal approach to teaching that can enhance student learning and understanding [32].

Approaches to Assessment

In a few cases, rubrics were used to assess the student projects, often consisting of a list of specific requirements for the project and points associated with each requirement.

  • “I do try to develop some scoring grids (for) presentations … . I'm going to have them do a presentation, what do I expect from them? Did they give a clear presentation? Did they understand the biological function of the protein? Did they do a good job of pointing out the structural nature of the protein or macromolecular system? Did they show three important noncovalent interactions?”

However, most of the interviewees assessed the student projects subjectively rather than using validated assessment instruments. Grades were assigned based on the overall quality of the project, a subjective assessment of student learning, and the complexity of the project outcome.

  • “No, I don't (have a rubric) … I really get a sense of their understanding by the quality of their renderings of the molecule… Three buttons will probably not be enough to tell your story … fifteen buttons is probably too much detail.”
  • “(If) they came, put in a good amount of time on it … it was a way to give them a little boost … and have them learn at the same time.”

A common thought among the interviewees was that they would like to use more formal rubrics, but their development can be challenging since the outcomes of molecular visualization are diverse and difficult to interpret on a quantitative scale (see quote in the left quadrant of Fig. 3).

Figure 3.

Recurring themes from surveys and interviews are typified by the quotes shown here.

Several interviewees mentioned specific questions or concepts that they thought were important in probing the students’ understanding of molecular visualization. For example, it is important that students understand the limitations of molecular visualization programs (i.e., what the software shows and what it does not or cannot show). One example of a limitation that many of the programs have is the inability to efficiently demonstrate dynamics, motions, and protein-protein or protein-ligand interactions. A second example of an important molecular visualization concept is the translation of molecules both horizontally (the same protein in different renderings/representations) and vertically (a protein in the context of biological organization- atoms, molecules, cells, organism). As mentioned before, the use of physical models alongside molecular visualization can aid in solidifying the concept of “sizing” a protein in biological context. In addition, the course structure often dictates the concepts that are most important for student learning. For example, courses which emphasize use of the literature and scientific writing may use molecular visualization as an aid in “telling a good story” about the molecule, while advanced biophysical and structural biology courses may require students to understand active site dynamics and chemical properties at a more detailed level.

A number of major themes emerged during the interviews. The quotes in Fig. 3 nicely summarize recurring concerns regarding student attitudes, challenges in dealing with software, evaluation of student learning with molecular visualization, and the need for broader, more uniform support for the pedagogy of teaching with these tools.

Wish List

Many of the interviewees described their molecular visualization “wish lists.” One of the most common requests was for an online central repository for molecular visualization activities, effective methods of assessment, rubrics, demos, and links to resources such as the Online Macromolecular Museum and other molecular visualization tools (with pros and cons listed for each program or tool). Such a repository could also provide a list of molecules that are best used to demonstrate differences between active/inactive states and ligand-induced conformational changes. Several interviewees also requested better and more cost-effective physical models, including those created by 3D printers. Others focused their wish lists on the capabilities of the molecular visualization software: requests were made for easier templates to create useful molecular visualization tutorials and for simple point-and-click access for morphing between different protein conformations and visualizing such features as a protein's active site and docking interactions between proteins, proteins and DNA/RNA, and proteins and ligands. Several interviewees requested easier access to their preferred molecular visualization program without having to purchase or obtain special licensing, particularly with PyMOL. Others asked for access to their preferred molecular visualization programs on their mobile devices so that students could easily access the programs during class. While some of the requested features are available on freeware programs and web sites, it was clear from the surveys and interviews that some of the participants were not aware of these features.


It should be noted that all of the survey and interview participants are active practitioners of molecular visualization, so the results are from a self-selected group who are already contributing members of the community. Participants ranged from graduate students to faculty members with decades of experience, with roughly half at the associate or full professor rank and 70% that had been using molecular visualization for more than 5 years. They used all the currently popular operating systems and had a wide variety of preferences for many of the molecular visualization programs that are available, although Jmol was clearly the most popular program, followed by PyMOL. Most users indicated that they used molecular visualization in biochemistry and cell biology courses, but it is likely that the distribution of course selections was skewed by our selection of target audience. Molecular visualization is used most often in demonstrations, though many incorporated visualization in homework assignments, exams or student projects. In both the surveys and the interviews, participants enthusiastically advocated for the use of molecular visualization in the classroom; some even claimed that this had changed or revitalized the way that they teach. At the same time, every one of these passionate advocates spoke at length about difficulties they had encountered along the way (Fig. 3). Respondents repeatedly commented on the challenge of assessing student learning with molecular visualization, with no clear consensus on the best approach to assessment. In summing up the results of the survey and the interview, we also found an extensive “wish list” by the respondents, with the most common being expanded features of the software, portability to other formats (smart phones and tablets), point-and-click access to information-rich models of proteins, full multi-media implementations that can add audio and video features to molecular visualization, and a central repository of well-tested molecular visualization assignments and assessment tools. Many of the interviewees considered themselves “early adopters” of the technology who were accustomed to breaking new ground. In general, the community seems ready to develop a more mature and uniform approach to using molecular visualization, particularly in the area of assessment.

The approaches for measuring student learning using molecular visualization appeared to fall into four broad categories, which will be listed from most to least common. The first of these was the usual written examination without images. Regardless of format, this was intended to be comprehensive over the material covered in that section of the course regardless of whether it was covered in lecture or in a visualization exercise. The second most common type of learning assessment was the problem set, whether used in or out of class. These required students to answer written questions and make predictions using molecular images, either static or interactive, as a source of information. The third type was a more in-depth use of static images. One interviewee used exam questions coupled to projected images. Other examples included the student capture of static images from an interactive molecular visualization to answer specific questions. More probing versions of this type of assessment included student interpretation of a static image, either verbally or in writing. Such interpretation could be in free form or take the form of student annotation such as labeling, captioning, and narrative embedding.

The most labor-intensive form of student use of molecular visualization was the student project. In its simplest form, this involved a written report, usually including a literature review of a topic illustrated with static images. This was in essence, a well-illustrated term article. A more comprehensive project involving molecular visualization would be a bioinformatics project which incorporated a significant structural biology component. The best example of this used by our interviewees was the project described by Feig and Jabri [33]. The type of project most focused on molecular visualization was one involving student authorship of annotated, interactive images to tell a molecular story. Published examples of this include Kinemage [34, 35], Chime [11], Jmol [14], and Proteopedia [27] authorship. A variety of criteria were used to assess student learning in these student projects. In terms of the technical aspects, students were required to meet the technical guidelines provided by the instructor, (i.e. buttons, annotations, colors, multiple renderings, etc.). In terms of content, the molecular narrative was expected to include details of the structure/function relationship as well as putting the structure in a physiological context. Finally, many student projects included an oral presentation in which the ability of the student to orally explain the project and answer questions was assessed either informally or via a scoring “grid” or rubric.

Aside from presentation of grading rubrics, few respondents to either the survey or the interviews used a well-defined instrument such as a rubric to assess student learning with molecular visualization. However, it became clear that two different types of instruments would be needed to properly assess student learning with molecular visualization. The first type would be an assessment of the content knowledge conveyed by the visualization. Our prior publication of a biomacromolecular 3D proficiency rubric in the Spring 2010 PDB Newsletter gave several examples of structural content from which individual instructors could devise more focused assessment instruments suitable for their particular instructional needs [36].

A second type of instrument would assess the unique understanding of structural biology accessible through interactive models, whether graphic or physical. To quote from Jane and David Richardson, “Molecular graphics use in biochemistry teaching has two complementary goals: to enhance learning of the subject matter and to develop analytical skills of a new sort” [37]. These new skills involve expertise in interacting with and extracting information from the model. Expertise of this type would involve things such as mental decoding of the symbolism embedded in the model, the ability to integrate multiple inputs (multimodality), and an understanding of the artistry of the model (use of color, depth cueing, etc). Further, such expertise would require an understanding of the limitations of the model itself as well as the experimental limitations of the information on which the model is based. Some of these are touched on by the proficiency rubric mentioned above, but the best approach to this type of molecular 3D literacy will likely require probing of the student thinking process as they interact with the model and attempt to construct their own mental model. While our survey indicates that many faculty members engage in this type of probing in an informal manner, we recommend two excellent articles by Schönborn and Anderson [38, 39] for advice on this approach.

A third type of instrument is not one intended to assess student learning directly, but rather one that could be useful to instructors in evaluating the educational potential of molecular visualization software. While our survey indicated that Jmol and PyMOL are currently the most popular molecular visualization programs for educational use, several other programs are used for specific instructional purposes. Examples of this are the use of Chimera to generate anaglyph images [40], the use of the Molecular Operating Environment in student projects involving bioinorganic and computational chemistry of heme proteins [41], the use of DeepView to superimpose multiple structures or perform homology modeling [19], and the comparison of the relative educational value of structure visualization and simulations [42].

In addition to the above feature-specific uses, computer software will eventually become obsolete and unsupported, as the Chime to Jmol transition illustrates [12], forcing a switch away from a familiar program. Many biochemistry educators are familiar with the software they used during their own education and research experiences and find this the easiest to use when they become teachers themselves. A software comparison with an emphasis on the educational capabilities of each program would be useful to all instructors in choosing the right tool for their particular pedagogical approach. We are currently in the process of designing and student testing such a comparative tool.


  • “Without visualization, I don't think my job would be nearly as much fun.”

This quote from an interviewee typifies responses from both the surveys and the interviews. Responses, even negative ones, clearly demonstrated the passion of the practitioners. With this enthusiasm also came a desire to understand how to use molecular visualization in the most effective manner.

It is clear that assessment of the effectiveness of a variety of molecular visualization teaching approaches in enhancing student learning of content knowledge as well as the attainment of new analytical skills will remain an important area of biochemistry education research. Finally, many respondents wanted access to a core set of molecular visualization resources that support biochemistry education at the undergraduate level. While several individuals and small teams maintain websites of very useful educational resources, e.g. molviz.org, perhaps it is time to begin developing a more comprehensive set of resources that include lesson plans and learning objectives as well as educationally sound and validated assessment tools available for all who use models of any kind to teach the wonders of the biomolecular world.


The authors thank Deborah Booth, Christine Zardecki and Eric Martz for their assistance in refining our survey. They also greatly appreciate the time given to them by the interview participants and their enthusiasm for teaching with molecular visualization. Finally, they thank Trevor Anderson for comments on the manuscript.

  1. 1

    For simplicity, percentages are reported as whole numbers and may not add up to exactly 100%.

Appendix A: Survey on Educational Uses of Molecular Visualization

Informed Consent

You are invited to participate in a survey activity designed by Paul Craig, Bob Bateman, and Lea Michel that has been designed for the biochemistry and molecular biology community to get a more systematic idea of how we use molecular visualization in education. The results of the survey will be presented at scientific conferences in addition to being submitted as a manuscript to a science education journal.

If you choose to take part, you will be asked to complete 11 multiple choice questions and 3 open ended questions, where many of the multiple choice questions also include a comment box to address concerns that may not be adequately covered in the multiple choice format. It has been suggested that the survey will take ∼15–20 min to complete.

Your participation in this project is voluntary and you are free to decline to participate, without consequence, at any time prior to or at any point during the activity. Any information you provide will be kept confidential, used only for the purposes of completing this assignment, and will not be used in any way that can identify you.

Please keep a copy of this consent form for your records. If you have other questions concerning your participation in this project, please contact us:

Paul Craig

Professor of Biochemistry and Bioinformatics

Rochester Institute of Technology

85 Lomb Memorial Drive

Building 75, Room 3159

Rochester, NY 14623

Telephone: 585-475-6145

Thank you for your participation in our project.


Paul Craig, Robert Bateman and Lea Vacca Michel

Survey Questions

  1. After you have read the information above, you can indicate your consent to participate in the survey by selecting “Yes”. You can then proceed to the survey by clicking “Next”. If you elect not to participate in the survey, you can select “No”. The survey will then close when you click on “Next”.
  2. What is your academic rank? (one answer only)

    1. Graduate Student

    2. Post-Doctoral Fellow
    3. Lecturer
    4. Assistant Professor
    5. Associate Professor
    6. Full Professor
  3. What operating system do you normally use? (more than one answer allowed)

    1. Windows XP

    2. Windows Vista
    3. Windows 7
    4. Mac OS X
    5. Linux
  4. How often do you use 3D molecular structures in your courses? Please select the one best answer. (one answer only)

    1. >10X per year

    2. 5-10X per year
    3. 1-4X per year
    4. Never
  5. How long have you been using Molecular Visualization in the classroom? (one answer only)

    1. More than 15 years

    2. Between 10 and 15 years
    3. Between 5 and 10 years
    4. Less than 5 years
  6. In which courses do you use 3D molecular visualization? (more than one answer allowed)

    1. General Biology

    2. Cell Biology
    3. Molecular Biology
    4. Biochemistry
    5. Pharmacology
    6. Organic Chemistry
    7. Other (open box for free form response)
  7. Which 3D molecular visualization program(s) do you use? (Respondents could check one option (used in the past, currently use sometimes, or currently use most of the time) for each program.

    ProgramUsed in the pastCurrently use sometimesCurrently use most of the time
    DeepView (Swiss PDB Viewer)   
    Protein Explorer   
    FirstGlance in Jmol   
    RCSB PDB Protein Workshop   

    Other (please specify) (open box for free form response).

  8. How do you use molecular visualization? (users could select as many options as they wished.

    1. As demonstrations in my classes

    2. As Supporting Information online resources for students to view outside of class
    3. As required online resources for students to view outside of class
    4. As required online resources for students to view outside of class. Students are tested on their knowledge of 3D structures
    5. As demonstrations in my labs
    6. As Supporting Information online resources for students to view outside of lab
    7. As required online resources for students to view outside of lab
    8. As required online resources for students to view outside of lab. Students are tested on their knowledge of 3D structures
    9. For research only
    10. Other (open box for free form response)
  9. Have you attempted to assess molecular visualization in your courses? If you have a grading rubric, we would be like you to email it to paul.craig@rit.edu.

    1. No. There is nothing to grade - the students are simply observers as I demonstrate

    2. No. I would like to assess their learning, but do not have a rubric for assigning grades.
    3. No, I used to grade them on this, but found it too difficult to assess or to grade consistently.
    4. Yes, but only conversationally to see if the students think it is helpful.
    5. Yes. I use a grading rubric (please attach it to your survey) but only for information purposes - it does not affect their grades.
    6. Yes. I use a grading rubric and it counts for less than 2% of their grade in the course.
    7. Yes. I use a grading rubric and it counts for between 2% and 5% of their grade in the course.
    8. Yes. I use a grading rubric and it counts for between 5% and 10% of their grade in the course.
    9. Other (open box for free form response)
  10. In which of the following settings have your students created 3D molecular visualization resources?

    1. None

    2. In my research group
    3. As optional class exercises
    4. As required class exercises
    5. To build a web site
    6. To contribute to Proteopedia or another online community
    7. Other (open box for free form response)
  11. How happy are you with the visualization program you are currently using? Please check boxes under the columns for the program(s) you are currently using. Users were given a choice of Jmol, Rasmol/RasTop, PyMOL, MolMol, CN3D, DeepView, Kinemage/KING, Protein Explorer and Other and were allowed to identify themselves as Extremely satified with one program, Satisfied with one program, Neutral/indifferent with one program, Dissatisfied with one program and Disgruntled and ready to go postal with one program. In addition, they was an open box for a free form response.

  12. How do you obtain molecular visualization resources for your classes? Respondents were allowed to choose as many options as they considered appropriate.

    1. I create them myself

    2. I find them on molvisindex.org
    3. I look through Eric Martz's MolviZ.Org site
    4. I find them through the PDB
    5. I search for them in Google
    6. I find them in Youtube
    7. Other (open box for free form response)

      Open-ended questions: No choices were provided and users were given a text box for free form answers.

  13. What additional resources would you like to have available to teach molecular structures?

  14. What would you like to be able to do with 3D molecular visualization programs that you currently cannot do?

  15. Is there another question you would like to answer or another comment you would like to submit?

Appendix B: Interview on Educational Uses of Molecular Visualization

Informed Consent

You are invited to participate in a survey activity designed by Paul Craig, Bob Bateman and Lea Michel that has been designed for the biochemistry and molecular biology community to get a more systematic idea of how we use molecular visualization in education. The results of the survey will be presented at scientific conferences in addition to being submitted as a manuscript to a science education journal.

If you choose to take part, you will be asked to complete 11 multiple choice questions and 3 open ended questions, where many of the multiple choice questions also include a comment box to address concerns that may not be adequately covered in the multiple choice format. It has been suggested that the survey will take approximately 15-20 minutes to complete.

In addition to the survey, you may also be asked to participate in an interview which may be conducted in person, by telephone or by one of several video chat tools available on the Internet (e.g., Skype or ooVoo). The interview should last 20 – 30 minutes and will reiterate some of the questions from the survey. Then we will delve deeper into your experience with students, with a focus on how the students interact with and/or create molecular visualization resources. We will never identify students by name or other identifiers during the interview or in any of our documentation. We will also explore your use of assessment and your plans for assessment tools in the future. Since you will provide more information about yourself (with possible identifiers), interview results will be presented in aggregate, with no identifying information to assure your anonymity. In reporting our results, we may choose to directly quote you, but you will not be identified in any reports or presentations of our results.

Your participation in this project is completely voluntary and you are free to decline to participate, without consequence, at any time prior to or at any point during the activity. Any information you provide will be kept confidential, used only for the purposes of completing this assignment, and will not be used in any way that can identify you.

Please keep a copy of this consent form for your records. If you have other questions concerning your participation in this project, please contact us:

Paul Craig

Professor of Biochemistry and Bioinformatics

Rochester Institute of Technology

85 Lomb Memorial Drive

Building 75, Room 3159

Rochester, NY 14623

Telephone: 585-475-6145

Thank you for your participation in our project.


Paul Craig, Robert Bateman and Lea Vacca Michel

Sample Interview Questions

This interview is intended to be an open exchange of ideas about molecular visualization. We would like to learn about your ideas and experiences, as well as what you like to give to and receive from the molecular visualization community.

  1. What is your academic rank? (taken directly from the survey).
  2. Please describe your institution. Possible answers include but are not limited to Research University, Comprehensive University (offers M.S., but few or no Ph.D. degrees) or Primarily Undergraduate Institution.
  3. What is your field of study?
  4. How many years have you been using molecular visualization? (taken directly from the survey).
  5. What is your preferred operating system? (taken directly from the survey).
  6. Please tell us a bit about your journey in using molecular visualization. When did you start? What programs have your tried? What is your preferred molecular visualization program?
  7. Are your students required to do a project using molecular visualization? If so, what does that project involve?
  8. Do your students work with physical models of macromolecules in your courses? Are they required to compare the physical models with computer visualizations?
  9. What forms of assessment do you normally use for your courses?
  10. Have you attempted to use molecular visualization in your assessment? If so, please describe what you have found.
  11. Do you have a rubric for assessment that incorporates molecular visualization?
  12. Do you have a rubric for assessment of student learning with molecular visualization that includes creation of resources (students preparing their own molecular visualizations)?
  13. What additional resources would you like to have available to teach molecular structures? (open ended; taken directly from the survey).
  14. What would you like to be able to do with 3D molecular visualization programs that you currently cannot do? (open ended; taken directly from the survey).