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

George Green soyo.green at gmail.com
Fri Nov 20 17:29:07 PST 2015


Know this has been a while, but just came back to it after a long while.
Got most of your suggestions working, but cannot get water-water hbonds
going. After some investigation, I think this could be due to the fact that
I'm using TIP4-EW water. Reason is that I got water-water hbonds working
with TIP3 and after trying lots of permutations cannot get this going.

My current per-frame script command for showing Hbonds is:
select :159-165.*; hbonds line 5 color gold  selRestrict any reveal true;
setattr p color gold :159-165.*;
setattr g lineType 1

This works fine in that hbonds between water and protein/ligand residues
are shown, but none between the water which is a problem.

Any advice would be greatly appreciated. :)

On Tue, May 19, 2015 at 8:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi George,
> With “retain true” you could have both the old and new H-bonds in the same
> place, but only see the old colors if the new ones are “underneath.”
> Instead I would say just use “hbonds” one time per frame and then re-color
> the desired lines with “setattr”, for example something like:
> hb line 5 color gold
> setattr p color red :64,80,76,50,21
> The latter command sets the “color” attribute of pseudobonds to red,
> affecting only the pseudobonds between atoms of the specified residues.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> 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 19, 2015, at 11:47 AM, George Green <soyo.green at gmail.com> wrote:
> >
> > 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
> > ############
> >
> >
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