Chimera-dev July 2016

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chimera-dev@cgl.ucsf.edu

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2 discussions

B factor
by Bashayer Althufairi 27 Jul '16

27 Jul '16

Hello As you know many crystallographers need to determine the ave. B factor of selected amino acids or sometimes they wanna know B factor of N-termius Vs. C-terminus of a protein. I'm working on a protein where I need to predict B factor of certain amino acids sequence as well as difference between the values for analysis. Is this possible by Chimera? If yes, I'd like to know Please the way step be step, If no, I wish you could recommend a simple way to do it by educational simple software like PyMol. Thank You in Advance -- Bashayer Althufairi Medicinal Chemistry department Virginia Commonwealth University

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Help with chimera extension for 3D printing
by Stephen Norris 20 Jul '16

20 Jul '16

Hello Chimera developers! I'm a recent graduate of URI where I worked as part of a 3D printing group working on molecular visualization. You can see some examples of our work at http://web.uri.edu/pharmacy/3d/3d-gallery/ . When we started the program we used both Jmol and Chimera on individual models but ever since Tom added the struts commands we've been 100% using Chimera and loving it! However as I'm ending my personal involvement in projects there, I still want to do one last thing which is to solve a major headache for the 3D printing process. When developing model in Chimera we cannot really determine what scale the model and it's components like strut diameter will be when printing. These scales can only really be determined once we import the model into the 3D printing software and set an overall scaling for the model. This is a problem as we can easily make a model which looks nice but when we determine the overall scale the struts may turn out to be too thin, and then we have to go back and re-export the model until we get them acceptable. In addition is no way to relate the scale of a model shown in the viewing window to an actual scale we could input to the computer software. The solution would be to have functionality in Chimera to work with the model and scale things in terms of real-life units. A program like solidworks would easily let one do this but for Chimera units are somewhat arbitrary. One trick with the 3D printing software is that the print bed is shown with a grid of units so we can expand the ortho view until the screen is showing the objects to be printed at their actual real life sizes. I've already developed an extension to do this in Chimera and a side effect is that the scale to input to the printer to get a model at the scale displayed on the screen is easily obtained. I've made a github repo for the extension at https://github.com/gerbi7/UCSF-Chimera-RealScale-Extension . So now I'm running into two problems which could use some expert advice or ideas: 1. It would be good to be able to export models with the scaling pre-applied so that one just has to select the correct unit when importing to the 3D printing software. As far as I can tell most of the export functionality is in C++ and doesn't include support for applying a global scale to an export. Since it's in C++ I don't know if this would be viable as an extension to modify it. So far my idea would be to modify the outputted file? 2. It would be incredibly useful if one could set style parameters such as ribbon width, strut widths, etc in terms of real-life units, and have them stay constant while the user can modify the overall scale of the model by zooming in and out. It would be good if there was some elegant way of doing this instead of brute-force setting every parameter whenever the zoom changes. As a side note if it was possible to just insert a scaling factor whenever an atom coordinate is needed for graphics purposes that would probably work to solve both problems but I doubt that exists currently. I look forward to hearing back from you. Stephen Norris

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