path: root/2021/captions/molecular.md

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# Transcript

[[!template text="Hi, I'm Blaine Mooers." start="00:00:00.880" video="mainVideo" id=subtitle]]
[[!template text="I'm going to be talking about" start="00:00:02.446" video="mainVideo" id=subtitle]]
[[!template text="the use of molecular graphics in Org" start="00:00:04.160" video="mainVideo" id=subtitle]]
[[!template text="for the purpose of doing" start="00:00:07.919" video="mainVideo" id=subtitle]]
[[!template text="reproducible research in structural biology." start="00:00:08.880" video="mainVideo" id=subtitle]]
[[!template text="I'm an associate professor of biochemistry" start="00:00:11.840" video="mainVideo" id=subtitle]]
[[!template text="and microbiology at the University of Oklahoma" start="00:00:13.722" video="mainVideo" id=subtitle]]
[[!template text="Health Sciences Center in Oklahoma City." start="00:00:15.768" video="mainVideo" id=subtitle]]
[[!template text="My laboratory uses X-ray crystallography" start="00:00:17.760" video="mainVideo" id=subtitle]]
[[!template text="to determine the atomic structures" start="00:00:19.600" video="mainVideo" id=subtitle]]
[[!template text="of proteins like this one" start="00:00:21.920" video="mainVideo" id=subtitle]]
[[!template text="in the lower left, and of nucleic acids" start="00:00:23.439" video="mainVideo" id=subtitle]]
[[!template text="important in human health." start="00:00:26.080" video="mainVideo" id=subtitle]]
[[!template text="This is a crystal of an RNA," start="00:00:27.840" video="mainVideo" id=subtitle]]
[[!template text="which we have placed in this" start="00:00:29.591" video="mainVideo" id=subtitle]]
[[!template text="X-ray diffraction instrument." start="00:00:31.359" video="mainVideo" id=subtitle]]
[[!template text="And after rotating the crystal" start="00:00:33.200" video="mainVideo" id=subtitle]]
[[!template text="in the X-ray beam for two degrees," start="00:00:35.600" video="mainVideo" id=subtitle]]
[[!template text="we obtain this following diffraction pattern," start="00:00:38.000" video="mainVideo" id=subtitle]]
[[!template text="which has thousands of spots on it." start="00:00:40.480" video="mainVideo" id=subtitle]]
[[!template text="We rotate the crystal for over 180 degrees," start="00:00:43.280" video="mainVideo" id=subtitle]]
[[!template text="collecting 90 images to obtain all the data." start="00:00:47.840" video="mainVideo" id=subtitle]]
[[!template text="We then process those images" start="00:00:51.760" video="mainVideo" id=subtitle]]
[[!template text="and do an inverse Fourier transform" start="00:00:56.000" video="mainVideo" id=subtitle]]
[[!template text="to obtain the electron density." start="00:00:57.752" video="mainVideo" id=subtitle]]
[[!template text="This electron density map has been" start="00:00:59.920" video="mainVideo" id=subtitle]]
[[!template text="contoured at the one-sigma level." start="00:01:01.888" video="mainVideo" id=subtitle]]
[[!template text="That level's being shown by" start="00:01:04.344" video="mainVideo" id=subtitle]]
[[!template text="this blue chicken wire mesh." start="00:01:06.116" video="mainVideo" id=subtitle]]
[[!template text="Atomic models have been fitted" start="00:01:08.640" video="mainVideo" id=subtitle]]
[[!template text="to this chicken wire." start="00:01:10.152" video="mainVideo" id=subtitle]]
[[!template text="These lines represent bonds between atoms," start="00:01:11.119" video="mainVideo" id=subtitle]]
[[!template text="atoms are being represented by points." start="00:01:14.240" video="mainVideo" id=subtitle]]
[[!template text="And atoms are colored by atom type," start="00:01:16.240" video="mainVideo" id=subtitle]]
[[!template text="red for oxygen, blue for nitrogen," start="00:01:18.640" video="mainVideo" id=subtitle]]
[[!template text="and then in this case," start="00:01:21.280" video="mainVideo" id=subtitle]]
[[!template text="carbon is colored cyan." start="00:01:23.040" video="mainVideo" id=subtitle]]
[[!template text="We have fitted a drug molecule" start="00:01:24.720" video="mainVideo" id=subtitle]]
[[!template text="to the central blob of electron density" start="00:01:27.203" video="mainVideo" id=subtitle]]
[[!template text="which corresponds to that active site" start="00:01:29.360" video="mainVideo" id=subtitle]]
[[!template text="of this protein, which is RET Kinase." start="00:01:32.400" video="mainVideo" id=subtitle]]
[[!template text="It's important in lung cancer." start="00:01:35.759" video="mainVideo" id=subtitle]]
[[!template text="When we're finished with model building," start="00:01:37.439" video="mainVideo" id=subtitle]]
[[!template text="we will then examine" start="00:01:40.079" video="mainVideo" id=subtitle]]
[[!template text="the result of the final structure" start="00:01:41.339" video="mainVideo" id=subtitle]]
[[!template text="to prepare images for publication" start="00:01:43.006" video="mainVideo" id=subtitle]]
[[!template text="using molecular graphics program." start="00:01:45.200" video="mainVideo" id=subtitle]]
[[!template text="In this case," start="00:01:47.439" video="mainVideo" id=subtitle]]
[[!template text="we've overlaid a number of structures," start="00:01:48.108" video="mainVideo" id=subtitle]]
[[!template text="and we're examining the distance between" start="00:01:50.000" video="mainVideo" id=subtitle]]
[[!template text="the side chain of an alanine" start="00:01:53.600" video="mainVideo" id=subtitle]]
[[!template text="and one or two drug molecules." start="00:01:55.680" video="mainVideo" id=subtitle]]
[[!template text="This alanine sidechain actually blocks" start="00:01:58.880" video="mainVideo" id=subtitle]]
[[!template text="the binding of one of these drugs." start="00:02:00.719" video="mainVideo" id=subtitle]]
[[!template text="The most popular program" start="00:02:02.159" video="mainVideo" id=subtitle]]
[[!template text="for doing this kind of analysis" start="00:02:03.439" video="mainVideo" id=subtitle]]
[[!template text="and for preparing images" start="00:02:06.320" video="mainVideo" id=subtitle]]
[[!template text="for publication is PyMOL." start="00:02:07.280" video="mainVideo" id=subtitle]]
[[!template text="PyMOL was used to prepare these images" start="00:02:09.520" video="mainVideo" id=subtitle]]
[[!template text="on the covers of these featured journals." start="00:02:11.440" video="mainVideo" id=subtitle]]
[[!template text="PyMOL is favored because" start="00:02:14.720" video="mainVideo" id=subtitle]]
[[!template text="it has 500 commands" start="00:02:17.520" video="mainVideo" id=subtitle]]
[[!template text="and 600 parameter settings" start="00:02:19.520" video="mainVideo" id=subtitle]]
[[!template text="that provide exquisite control" start="00:02:22.128" video="mainVideo" id=subtitle]]
[[!template text="over the appearance of the output." start="00:02:23.360" video="mainVideo" id=subtitle]]
[[!template text="PyMOL has over 100,000 users," start="00:02:24.959" video="mainVideo" id=subtitle]]
[[!template text="reflecting its popularity." start="00:02:28.480" video="mainVideo" id=subtitle]]
[[!template text="This is the GUI for PyMOL." start="00:02:30.000" video="mainVideo" id=subtitle]]
[[!template text="It shows in white the viewport area" start="00:02:31.599" video="mainVideo" id=subtitle]]
[[!template text="where one interacts" start="00:02:35.120" video="mainVideo" id=subtitle]]
[[!template text="with the loaded molecular object." start="00:02:36.080" video="mainVideo" id=subtitle]]
[[!template text="We have rendered the same RET kinase" start="00:02:37.840" video="mainVideo" id=subtitle]]
[[!template text="with a set of preset parameters" start="00:02:41.920" video="mainVideo" id=subtitle]]
[[!template text="that have been named &quot;publication&quot;." start="00:02:49.788" video="mainVideo" id=subtitle]]
[[!template text="The other way of applying" start="00:02:51.200" video="mainVideo" id=subtitle]]
[[!template text="parameter settings and commands" start="00:02:52.720" video="mainVideo" id=subtitle]]
[[!template text="is to enter them at the PyMOL prompt." start="00:02:54.319" video="mainVideo" id=subtitle]]
[[!template text="Then the third way is to load and run scripts." start="00:02:56.720" video="mainVideo" id=subtitle]]
[[!template text="PyMOL is actually written in C for speed," start="00:03:00.159" video="mainVideo" id=subtitle]]
[[!template text="but it is wrapped in Python for extensibility." start="00:03:03.120" video="mainVideo" id=subtitle]]
[[!template text="In fact, there are over 100 articles" start="00:03:06.159" video="mainVideo" id=subtitle]]
[[!template text="about various plugins and scripts" start="00:03:09.680" video="mainVideo" id=subtitle]]
[[!template text="that people have developed" start="00:03:11.599" video="mainVideo" id=subtitle]]
[[!template text="to extend PyMOL for years." start="00:03:12.400" video="mainVideo" id=subtitle]]
[[!template text="Here's some examples" start="00:03:15.120" video="mainVideo" id=subtitle]]
[[!template text="from the snippet library that I developed." start="00:03:16.480" video="mainVideo" id=subtitle]]
[[!template text="On the left is a default" start="00:03:18.959" video="mainVideo" id=subtitle]]
[[!template text="cartoon representation of a RNA hairpin." start="00:03:21.280" video="mainVideo" id=subtitle]]
[[!template text="I find this reduced representation" start="00:03:24.640" video="mainVideo" id=subtitle]]
[[!template text="of the RNA hairpin to be too stark." start="00:03:27.040" video="mainVideo" id=subtitle]]
[[!template text="I prefer these alternate ones" start="00:03:30.799" video="mainVideo" id=subtitle]]
[[!template text="that I developed." start="00:03:32.319" video="mainVideo" id=subtitle]]
[[!template text="So, these three to the right of this one" start="00:03:33.840" video="mainVideo" id=subtitle]]
[[!template text="are not available through" start="00:03:37.519" video="mainVideo" id=subtitle]]
[[!template text="pull downs in PyMOL." start="00:03:39.519" video="mainVideo" id=subtitle]]
[[!template text="So why developed a PyMOL" start="00:03:40.720" video="mainVideo" id=subtitle]]
[[!template text="snippet library for Org?" start="00:03:42.748" video="mainVideo" id=subtitle]]
[[!template text="Well, Org provides great support" start="00:03:44.879" video="mainVideo" id=subtitle]]
[[!template text="for literate programming," start="00:03:47.040" video="mainVideo" id=subtitle]]
[[!template text="where you have code blocks" start="00:03:48.560" video="mainVideo" id=subtitle]]
[[!template text="that contain code that's executable," start="00:03:49.840" video="mainVideo" id=subtitle]]
[[!template text="and the output is shown" start="00:03:52.000" video="mainVideo" id=subtitle]]
[[!template text="below that code block." start="00:03:53.040" video="mainVideo" id=subtitle]]
[[!template text="And then you can fill" start="00:03:54.959" video="mainVideo" id=subtitle]]
[[!template text="the surrounding area in the document" start="00:03:56.720" video="mainVideo" id=subtitle]]
[[!template text="with the explanatory prose." start="00:03:58.959" video="mainVideo" id=subtitle]]
[[!template text="Org has great support" start="00:04:00.799" video="mainVideo" id=subtitle]]
[[!template text="for editing that explanatory prose." start="00:04:02.000" video="mainVideo" id=subtitle]]
[[!template text="Org can run PyMOL through PyMOL's Python API." start="00:04:04.480" video="mainVideo" id=subtitle]]
[[!template text="One of the uses of such an Org document" start="00:04:08.080" video="mainVideo" id=subtitle]]
[[!template text="is to assemble a gallery of draft images." start="00:04:11.280" video="mainVideo" id=subtitle]]
[[!template text="We often have to look at" start="00:04:14.487" video="mainVideo" id=subtitle]]
[[!template text="dozens of candidate images" start="00:04:16.563" video="mainVideo" id=subtitle]]
[[!template text="with the molecule in different orientations," start="00:04:19.840" video="mainVideo" id=subtitle]]
[[!template text="different zoom settings," start="00:04:22.000" video="mainVideo" id=subtitle]]
[[!template text="different representations," start="00:04:23.520" video="mainVideo" id=subtitle]]
[[!template text="different colors, and so on." start="00:04:25.032" video="mainVideo" id=subtitle]]
[[!template text="And to have those images along with…," start="00:04:27.280" video="mainVideo" id=subtitle]]
[[!template text="adjacent to the code" start="00:04:30.639" video="mainVideo" id=subtitle]]
[[!template text="that was used to generate them," start="00:04:31.840" video="mainVideo" id=subtitle]]
[[!template text="can be very effective for" start="00:04:33.680" video="mainVideo" id=subtitle]]
[[!template text="further editing the code" start="00:04:37.199" video="mainVideo" id=subtitle]]
[[!template text="and improving the images." start="00:04:39.680" video="mainVideo" id=subtitle]]
[[!template text="Once the final images have been selected," start="00:04:40.880" video="mainVideo" id=subtitle]]
[[!template text="one can submit the code" start="00:04:44.080" video="mainVideo" id=subtitle]]
[[!template text="as part of the supplemental material." start="00:04:46.320" video="mainVideo" id=subtitle]]
[[!template text="Finally, one can use the journal package" start="00:04:48.479" video="mainVideo" id=subtitle]]
[[!template text="to use the Org files as" start="00:04:52.400" video="mainVideo" id=subtitle]]
[[!template text="an electronic laboratory notebook," start="00:04:54.608" video="mainVideo" id=subtitle]]
[[!template text="which is illustrated with molecular images." start="00:04:57.120" video="mainVideo" id=subtitle]]
[[!template text="This can be very useful" start="00:04:59.600" video="mainVideo" id=subtitle]]
[[!template text="when assembling manuscripts" start="00:05:01.039" video="mainVideo" id=subtitle]]
[[!template text="months or years later." start="00:05:04.080" video="mainVideo" id=subtitle]]
[[!template text="This shows the YASnippet pull down" start="00:05:05.440" video="mainVideo" id=subtitle]]
[[!template text="after my library has been installed." start="00:05:08.320" video="mainVideo" id=subtitle]]
[[!template text="I have an Org file open," start="00:05:12.720" video="mainVideo" id=subtitle]]
[[!template text="so I'm in Org mode." start="00:05:15.360" video="mainVideo" id=subtitle]]
[[!template text="We have the Org mode submenu," start="00:05:17.120" video="mainVideo" id=subtitle]]
[[!template text="and under it, all my snippets" start="00:05:20.880" video="mainVideo" id=subtitle]]
[[!template text="are located in these sub-sub-menus" start="00:05:23.919" video="mainVideo" id=subtitle]]
[[!template text="that are prepended with pymolpy." start="00:05:26.880" video="mainVideo" id=subtitle]]
[[!template text="Under the molecular representations menu," start="00:05:30.880" video="mainVideo" id=subtitle]]
[[!template text="there is a listing of snippets." start="00:05:33.840" video="mainVideo" id=subtitle]]
[[!template text="The top one is for the ambient occlusion effect," start="00:05:36.479" video="mainVideo" id=subtitle]]
[[!template text="which we're going to apply" start="00:05:38.563" video="mainVideo" id=subtitle]]
[[!template text="in this Org file." start="00:05:39.840" video="mainVideo" id=subtitle]]
[[!template text="So these lines of code were inserted after," start="00:05:41.039" video="mainVideo" id=subtitle]]
[[!template text="as well as these flanking lines" start="00:05:44.240" video="mainVideo" id=subtitle]]
[[!template text="that define the source block," start="00:05:48.479" video="mainVideo" id=subtitle]]
[[!template text="were inserted by clicking on that line." start="00:05:50.240" video="mainVideo" id=subtitle]]
[[!template text="Then I've added some additional code." start="00:05:53.280" video="mainVideo" id=subtitle]]
[[!template text="So, the first line defines" start="00:05:55.120" video="mainVideo" id=subtitle]]
[[!template text="the language that we're using." start="00:05:56.880" video="mainVideo" id=subtitle]]
[[!template text="We're going to use" start="00:05:59.039" video="mainVideo" id=subtitle]]
[[!template text="the jupyter-python language." start="00:05:59.768" video="mainVideo" id=subtitle]]
[[!template text="Then you can define the session," start="00:06:02.639" video="mainVideo" id=subtitle]]
[[!template text="and the name of this is arbitrary." start="00:06:04.560" video="mainVideo" id=subtitle]]
[[!template text="Then the kernel is our means" start="00:06:06.400" video="mainVideo" id=subtitle]]
[[!template text="by which we gain access" start="00:06:09.680" video="mainVideo" id=subtitle]]
[[!template text="to the Python API of PyMOL." start="00:06:11.360" video="mainVideo" id=subtitle]]
[[!template text="The remaining settings apply to the output." start="00:06:14.880" video="mainVideo" id=subtitle]]
[[!template text="To execute this code" start="00:06:17.039" video="mainVideo" id=subtitle]]
[[!template text="and to get the resulting image," start="00:06:18.319" video="mainVideo" id=subtitle]]
[[!template text="you put the cursor inside this code block," start="00:06:21.199" video="mainVideo" id=subtitle]]
[[!template text="or on the top line," start="00:06:25.120" video="mainVideo" id=subtitle]]
[[!template text="and enter Control c Control c (C-c C-c)." start="00:06:26.560" video="mainVideo" id=subtitle]]
[[!template text="This shows the resulting image" start="00:06:29.840" video="mainVideo" id=subtitle]]
[[!template text="has been loaded up." start="00:06:32.240" video="mainVideo" id=subtitle]]
[[!template text="It takes about 10 seconds for this to appear." start="00:06:33.600" video="mainVideo" id=subtitle]]
[[!template text="So the downside of this is" start="00:06:37.280" video="mainVideo" id=subtitle]]
[[!template text="if you have a large number of these," start="00:06:38.479" video="mainVideo" id=subtitle]]
[[!template text="the Org file can lag quite a bit" start="00:06:40.729" video="mainVideo" id=subtitle]]
[[!template text="when you try to scroll through it," start="00:06:43.919" video="mainVideo" id=subtitle]]
[[!template text="so you need to close up these result drawers," start="00:06:45.120" video="mainVideo" id=subtitle]]
[[!template text="and only open up the ones" start="00:06:48.319" video="mainVideo" id=subtitle]]
[[!template text="that you're currently examining." start="00:06:50.960" video="mainVideo" id=subtitle]]
[[!template text="These are features I think" start="00:06:53.199" video="mainVideo" id=subtitle]]
[[!template text="are important in practical work." start="00:06:54.319" video="mainVideo" id=subtitle]]
[[!template text="So, the plus is, a feature that's present," start="00:06:56.240" video="mainVideo" id=subtitle]]
[[!template text="minus is absent." start="00:06:59.840" video="mainVideo" id=subtitle]]
[[!template text="I think tab stops and tab triggers" start="00:07:01.120" video="mainVideo" id=subtitle]]
[[!template text="are really important." start="00:07:03.199" video="mainVideo" id=subtitle]]
[[!template text="Triggers are important for" start="00:07:04.800" video="mainVideo" id=subtitle]]
[[!template text="the fast assertion code," start="00:07:05.680" video="mainVideo" id=subtitle]]
[[!template text="tab stops are important for" start="00:07:06.720" video="mainVideo" id=subtitle]]
[[!template text="complete, accurate editing of code." start="00:07:08.639" video="mainVideo" id=subtitle]]
[[!template text="I already addressed the rendering speed" start="00:07:10.560" video="mainVideo" id=subtitle]]
[[!template text="and scrolling issue." start="00:07:12.735" video="mainVideo" id=subtitle]]
[[!template text="I think the way around this" start="00:07:14.560" video="mainVideo" id=subtitle]]
[[!template text="is just to export the Org document to a PDF file" start="00:07:15.759" video="mainVideo" id=subtitle]]
[[!template text="and do your evaluation of different images" start="00:07:19.199" video="mainVideo" id=subtitle]]
[[!template text="by examining them in the PDF" start="00:07:23.360" video="mainVideo" id=subtitle]]
[[!template text="rather than the Org file." start="00:07:25.199" video="mainVideo" id=subtitle]]
[[!template text="The path to PDF is lightning fast in Emacs" start="00:07:26.560" video="mainVideo" id=subtitle]]
[[!template text="compared to Jupyter," start="00:07:30.400" video="mainVideo" id=subtitle]]
[[!template text="where it's cumbersome in comparison." start="00:07:32.240" video="mainVideo" id=subtitle]]
[[!template text="This is a snapshot of my initialization file." start="00:07:35.280" video="mainVideo" id=subtitle]]
[[!template text="These parts are relevant to doing this work." start="00:07:38.400" video="mainVideo" id=subtitle]]
[[!template text="A full description of them" start="00:07:41.840" video="mainVideo" id=subtitle]]
[[!template text="can be found in the README file" start="00:07:43.039" video="mainVideo" id=subtitle]]
[[!template text="of this repository on GitHub." start="00:07:46.319" video="mainVideo" id=subtitle]]
[[!template text="I'd like to thank the" start="00:07:48.639" video="mainVideo" id=subtitle]]
[[!template text="Nathan Shock Data Science Workshop" start="00:07:49.456" video="mainVideo" id=subtitle]]
[[!template text="for feedback during presentations" start="00:07:51.840" video="mainVideo" id=subtitle]]
[[!template text="I've made about this work." start="00:07:54.319" video="mainVideo" id=subtitle]]
[[!template text="And I would also like to thank" start="00:07:56.160" video="mainVideo" id=subtitle]]
[[!template text="the following funding sources for support." start="00:07:57.628" video="mainVideo" id=subtitle]]
[[!template text="I will now take questions. Thank you." start="00:08:00.240" video="mainVideo" id=subtitle]]
[[!template text="captions by Blaine Mooers and Bhavin Gandhi" start="00:08:03.879" video="mainVideo" id=subtitle]]