[PyMOL] Still time to participate in the Teach-Discover-Treat 2014 Competition!

tools. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito

[PyMOL] Winners of the Teach-Discover-Treat 2014 Challenge

! The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito -- The best possible search technologies are now affordable for all companies. Download your

Re: [PyMOL] Is it possible to write PNG images in PyMOL of higher resolution than the viewing window?

Hi Brenton >From the PyMOL command line the PNG file creation/saving command is: PyMOL> png filename, width, height, dpi, ray=1 Notice that ray equals 1 to create a ray-traced image. The dpi option can be set to your desired resolution in dots-per-inch and the width and height options use the unit

Re: [PyMOL] visualize mode

Hi What about Modevectors? http://www.pymolwiki.org/index.php/Modevectors Emilio On Fri, Jun 19, 2015 at 10:23 AM, Command Line wrote: > Hi, that works for me. Albeit I would be more happy if there would be an > option directly inside pymol. Anyway, thanks. > > 2015-06-18 16:30 GMT-05:00 Osvald

[PyMOL] creating anaglyphic 3D images in PyMOL

Hi I know that I can create cross-eye stereo images with PyMOL but I was curious how to create anaglyphic (Red/Blue, Red/Cyan or Red/Blue-Green) 3D images similar to those created in Spartan. Other than post-processing the images with Photoshop, is there a way to have PyMOL natively construct thes

Re: [PyMOL] Detecting holes/cavities in surface

Hi Daniel CAVER is another possible PyMOL plugin http://www.caver.cz >From the CAVER website, "CAVER provides rapid, accurate and fully automated calculation of tunnels and channels in static and dynamic structures. The molecules amendable to analysis of CAVER include proteins, nucleic acids, or i

Re: [PyMOL] Transparent Background in Educational Version

Hi Cris Please include the ray=1 option in your png test.png, dpi=300 command or use the set opaque_background, off instead of the set ray_opaque_background, off command. Commands to create a PNG file with a transparent background: set opaque_background, off png test.png, dpi=300, ray=1 *PNG fi

Re: [PyMOL] get_area algorithm and dot_density accuracy

Hi The accuracy of the calculation depends on the dot_density value (the amount of sampling done) with 1 being the lowest quality and 4 being the best quality. A dot_density value of 1 uses less computational resources (time) than a dot_density of 4 because of the amount of sampling performed to ca

Re: [PyMOL] get_area algorithm and dot_density accuracy

lculations? DSSP > is likely to be using the rolling ball method. > > Regards. > > On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito > wrote: >> Hi >> The accuracy of the calculation depends on the dot_density value (the >> amount of sampling done) with 1 be