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

[George Green]

Hi Elaine,

Thanks for your detailed reply. Only just saw your email. I will test and
check. I think your tips should sort my problem out!

Many thanks!

On Thu, May 14, 2015 at 5:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> >
> > ################################################
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150517/c18ab427/attachment.html>