Dear all, I am using Jmol to generate a lot of rotated protein visualization images from a given PDB formatted file. In short, the script looks something like this:
zap pdbfile = "..." // path to the PDB file set antialiasImages on; var camlistX = [...] //list of 1000 rotation angles var camlistY = [...] //list of 1000 rotation angles var camlistZ = [...] //list of 1000 rotation angles load @pdbfile; color white; background black; cartoon only; cartoon off; backbone 1.0; color white; for (var i=1; i<=1000; i=i+1) // 1000 rotation. reset var rotX = camlistX[i]; var rotY = camlistY[i]; var rotZ = camlistZ[i]; rotate x @rotX; rotate y @rotY; rotate z @rotZ; filename = "x:/image-" + i + "v1.jpg"; write IMAGE 128 128 JPG 100 @filename; end for Then I repeat the for-loop for different type of visualization (ribbons, rockets, and cartoon). When using old version of Jmol (for example: Jmol-13.1.16_2013.05.20a), the process to generate 1000 rotations for 4 types of visualizations (4000 images) can be completed in a couple of minutes. However, if I used the newer version of Jmol (for example: Jmol-14.0.7, Jmol-14.2.9_2014.11.23, Jmol-14.3.11_2014.12.17) the same script took more than 1 hour to complete with very low cpu usage. As additional information, I am using Linux CentOS 6.5 with ramdisk (ramfs) to speed up the writing of the JPG files (because basically I only need to store the files temporarily and the files will be processed using Python soon afterwards). I used the following parameters when calling Jmol.jar: java -Xmx512m -jar Jmol.jar -s ./script.js -L -o -n -x Do I need some changes in my script to speed up the process in new version of Jmol? I would also appreciate if there is any suggestions to further speed up the process even in the old version of Jmol (I am wondering if there is a workaround so that I can obtain the rendered 2D images directly in Python without writing to disk). Thank you, Best regards, Chendra Hadi Suryanto ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
