[Chimera-users] Inter-molecular H-bonds between water molecules not displayed in per-frame script

Elaine Meng meng at cgl.ucsf.edu
Thu May 14 09:18:35 PDT 2015


Hi George,
I see at least one definite problem and suspect an additional problem.  It is impossible to tell for sure without having your data, which you should usually include with such a question to allow your problem to be reproduced so we don’t have to waste time guessing.

(1) The definite problem is that your “hbonds” command isn't using the selection in any way.  It simply acts on all atoms, which is fine if that’s what you want it to do.   But based on your description, it is not actually working on all atoms, so there must be some misunderstanding or incomplete description of what’s happening.  To limit “hbonds” to the selection, you’d need the “selRestrict” option.  See “hbonds” documentation for the possible values of that option:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>

It’s possible that hbonds is working on those waters but that they aren’t displayed due to suspected problem #2, below.  To force undisplayed items to be displayed if they are involved in H-bonds, you’d use the hbonds option “reveal true” … but that might accrete more and more displayed residues throughout your trajectory, so I’m not sure you would want it.  “intermodel” and “intramodel” are both default true so you don’t have to put them in your command.

Also, you don’t need to display the same stuff at every frame since presumably it was displayed in the previous frame.  You would just display it once at the beginning before running your per-frame script.

(2) The suspected secondary problem is that “:159-162” may not actually specify the waters, because if they don’t have a chain ID, Chimera automatically processes them into chain “water”.  Thus they may not be displayed by your first “disp” command that list residue numbers, but they will be displayed by the second one, “disp :WAT”.  Your select command may not be selecting them (try typing it in the command line to see) and in that case you’d need something like:

select :1-158:159-162.water
- OR  -
select :1-158:159-162.*
- OR -
select :1-158:wat
(where the latter would select all residues named WAT, so you’d only use that if there weren’t other WAT residues you didn’t want to show)

 The automatic processing into chain “water” was put into Chimera because some data had protein residues and water residues with the same residue numbers, and the added chain ID provided a handle for specifying them independently.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 14, 2015, at 7:42 AM, George Green <soyo.green at gmail.com> wrote:
> 
> Hi,
> I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below:
> 
> Water molecules are residues :159-162
> 
> I would be very grateful for any assistance. :)
> sg
> 
> ################################################
> ####################
> # per-frame H-bond
> repr bs :158
> color hot pink :158
> color byhet :158
> #
> disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162
> disp :WAT
> #
> select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select
> select :90
> 
> ################################################




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