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

[George Green]

Hi,

Just one other question if I could trouble you? Is it possible to have two
colors of H-bond in the per-frame script. That way I could highlight bonds
of particular importance (red), while the ones that maintain a steady
structure are yellow. That would help draw the users eye and save wordy
annotations. I tried the following to no avail. I suspect that maybe this
is not possible? If you could offer any guidance, I would be much obliged.
:)


###########
select :1-158; hbonds line 5 color gold ; ~select
select :64,80,76,50,21; hbonds selrestrict both retainCurrent true line 5
color red ; ~select
############



On Sun, May 17, 2015 at 3:13 AM, George Green <soyo.green at gmail.com> wrote:

> 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
>> >
>> > ################################################
>>
>>
>
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