Hi,
So I finally identified the source to this problem that I have been
having for almost a year now which is quoted below.
I wanted to post it here for other people that are having the same
issue. Through a process of elimination, I've determined that the
problem originates in the autodock vina plugin.
It seems that in the __init__() function of the plugin, the
"retain_order" setting is set. This seems to be the cause of the problem.
To reproduce:
$ pymol -k #don't load .pymolrc or plugins
fetch 1YCR
cmd.set("retain_order")
h_add 1YCR
Look at the sequence viewer, all of the hydrogens are listed first. And
if you save it as a pdb, all of the hydrogens are listed first and then
all of the heavy atoms. This causes problems with a number of other
programs.
Is there anyway around this issue other then unsetting retain_order
every time I want to add hydrogens to a structure or not having the
autodock plugin loaded?
I've cc'd the author of the plugin, Daniel Seeliger, hopefully he can
shed some light on whether this setting is necessary for the
functionality of the plugin.
Matt
*Re: [PyMOL] Problem with h_add hydrogens in sequence viewer
<http://ehc.ac/p/pymol/mailman/message/30647188/>*
From: Thomas Holder <thomas.holder@sc...> - 2013-03-26 13:06:08
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
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