Hi, 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; ~select 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@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@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 ############