Jmol users, exciting news on three fronts:
load FILTER selection of biomolecules from PDB files thermal (and otherwise) ellipsoids and spheres See http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.6#load and http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.6#ellipsoid load FILTER ----------- Jmol 11.5.33 allows a new way to load a file -- filtering atoms as the file is loaded so as to not require as much memory for large models. It's very simple. The syntax is similar to a SELECT command - but read the documentation, because it's not quite the same. For example: load 1sva.pdb FILTER "*.CA" Additional filters allow for selection of specific chains and specific group names. In addition, specific atom names, group names, and chains can be selected OUT using a ! character: load 1blu.pdb FILTER "![HOH]" selection of biomolecules from PDB files ---------------------------------------- Jmol 11.5.33 reads the REMARK 350 headers of PDB files, allowing reading of specific biomolecules constructed from specific chain sets and applied symmetry. The default is to apply the symmetry, but if you add the "NOSYMMETRY" flag, then the symmetry transformations are not applied. load 1sva.pdb FILTER "*.CA;BIOMOLECULE 1" As part of this, you can specify particular BIOMT transformations you want to apply: load 1sva.pdb FILTER "BIOMOLECULE 1,#1,#2,#3,#4,#5" (That's all the atoms in one virus capsid section -- 1/12 of the capsid.) thermal ellipsoids ------------------ Jmol 11.5.33 reads the Uij from PDB and CIF files and can display standard thermal ellipsoids in a variety of ways. It couldn't be simpler: load quartz.cif ellipsoids ON The default rendering is set ellipsoidBall TRUE but there are several different options discussed in the documentation. In addition, you can specify an ellipsoid at a particular point in space if you know the axes for the ellipsoid. These ellipsoids might be particularly valuable for producing spheres where no atom exists. For example: load 1sva.pdb FILTER "*.CA;BIOMOLECULE 1" color group set specular off ellipsoid virus CENTER {0 0 0} AXES {1 0 0} {0 1 0} {0 0 1} SCALE 170 color $virus yellow (The axes are all the same length, so this is a sphere.) In the context of the viral capsid discussed above, changing the scale of this sphere produces an interesting internal spherical clipping effect on visualization of the capsid. For example: ellipsoid virus AXES {1 0 0} {0 1 0} {0 0 1} scale 220 shows very nicely just the outermost section of the capsid. -Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
