Hi Matt, use the "sort" command after adding atoms:
PyMOL> h_add 1ycr PyMOL> sort See also: http://pymolwiki.org/index.php/Sort Cheers, Thomas Matthew Baumgartner wrote, On 03/26/13 13:59: > Hi, > When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr' > the hydrogens are added to the structure as expected, but they are put > in the sequence viewer as their own residue with the same chain. > > This is problematic for several reasons, one is that it breaks > selections, when I click on a heavy atom of a residue (in residue > selection mode) only the heavy atoms are selected and not the > hydrogens. Also, if I save the structure to an pdb file, all of the > hydrogens for the whole structure are placed at the beginning or the end > of the structure, which makes them difficult to be interpreted by other > programs (babel, chimera, namd, etc). > > I am using Pymol 1.5.0.1. (I will be updating to 1.6 soon). > > Any suggestions for settings to change or a workaround (possibly > involving other programs, if necessary), would be greatly appreciated. > > Thanks, > Matt -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
