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-Intelreg; 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
