I’m very happy to learn that Zeynep Kürkçüoğlu Soner, a scientist working on generating atomistic conformers for proteins with various size, saw this tutorial and adapted it for her purposes on PyMOL. Below is the result, with some Brightness increase in Photoshop. įor rendering, we preferred the Tachyon module, which generates files that can be opened in Photoshop. Step 5 – Set background color to white from MenuGraphicsColors, “Display” Category, “Background”. Select “Tube” with Radius “0.2” color it by a different Coloring Method and choose an opaque Material. Be sure to select the frame of your choice in the main screen). (We wanted to show the initial structure with red you may want to emphasize a different state. Step 4 – Make a copy of the representation (from Create Rep under Graphical Representations), this time displaying the initial structure only. We preferred white to black (“WBlk”, with offset “0.0”, midpoint “0.6”) because we wanted to show more clearly where the movement ends (on a white background). You can change this from MenuGraphicsColors, Categories box “Conformation” selection.
Step 3 – Make the Coloring Method “Timestep” (under “Trajectory”), also set the Material “Transparent”. This is achieved under the Trajectory tab, Draw Multiple Frames option, using the frame values “0:1:19” (since we have 20 frames). Step 2 – Show all trajectory snapshots at once. Step 1 – MenuGraphicsRepresentations, make the Drawing Method “Tube” and Radius “0.1”. These data should be written into a single pdb trajectory file, which is then read into VMD. (The first 20 frames out of a total of 100 seems to work fine for our system.) The initial file should have the average structure data as well as the mode vector added onto the average structure coordinates in pieces. I want to share this method with the world in detail for people who might want to use it. Below are our notes explaining the process in VMD. Below is a snapshot from a figure in that paper at the bottom you can see the motion visualization that we created.
#Vmd movie trace software#
This time Canan and I worked out a method (within the software VMD – Visual Molecular Dynamics) that we thought was more successful (and good-looking) than the arrows in showing which parts move to what degree and in which direction. The method I saw being used was putting in lots of red arrows/cones (one for each residue), and I wasn’t happy with how they looked ugly, busy, and uninformative.
I had had some previous experience with this problem in Image of Science 2010 in Ayşe Özlem Aykut’s project, and then in the Structural Biology class I took in Sabancı University. 41. There, I once again faced the challenge of showing protein dynamics in static images since scientists usually publish in static (printed) media, showing these motions in figures is a common problem because proteins are extremely complex structures and even drawing them without motion is a nightmare. First aired December 2019.In 2011 I worked with Canan Atılgan and Ali Rana Atılgan on the figures of their paper “ Network-based Models as Tools Hinting at Non-evident Protein Functionality” in Annual Review of Biophysics, Vol.UKTV Original series, produced by Red Production Company for UKTV’s Alibi channel and BBC Studios Distribution.It will be Sarah and Kathy’s exacting minds that reward Emma’s faith in the science that has fuelled her imagination, and who will ultimately bring her mother’s killer to justice. But why are Sarah Gordon (Laura Fraser), professor of chemistry, and Kathy Torrence (Jennifer Spence), professor of forensic anthropology, using her mother’s case for their course?ĭetermined to discover what happened to Marie but unable to get answers from her family, Emma turns to Sarah who offers up trusted friend DI McKinven (Michael Nardone) as the natural place for Emma to take her revelations.Īs Emma reconnects with her dad Drew (John Gordon Sinclair), her childhood friend Skye (Jamie Marie Leary) and her mum Izzy (Laurie Brett), while falling for the gentle and irresistible Daniel (Martin Compston), her sleuthing takes her into dark corners, unpicking more and more secrets, and it becomes clear that she should trust no-one. But having completed the first module, Emma knows exactly who the victim is: her mum! Marie Monroe (Carly Anderson) was murdered when Emma was seven, her body was discovered on Law Hill and no one has ever been convicted. Given a fictitious murder case, her task is to identify the victim and establish how they died. When Emma Hedges (Molly Windsor) returns to Dundee to start her new job as a lab technician, she’s encouraged to take part in an online course teaching the principles of forensic science.
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