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

Elaine Meng meng at cgl.ucsf.edu
Tue May 19 12:07:13 PDT 2015

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. 

I hope this helps,
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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