Re: [PyMOL] Problem with h_add hydrogens in sequence viewer

[Thomas H. <tho...@sc...>]

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