[Chimera-users] Inter-molecular H-bonds between water molecules not displayed in per-frame script
soyo.green at gmail.com
Fri Nov 20 17:47:32 PST 2015
AWESOME!!!!!! :) :) :)
Thanks v much. this was doing my head in for the last hour or so!!!
On Sat, Nov 21, 2015 at 1:40 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi George,
> Unfortunately the TIP4EW atoms are not recognized as H-bonding. You would
> have to delete the 4th point and remove the H1-H2 bond for them to be
> recognized as such. For example, commands:
> del @epw
> ~bond @h1,h2
> Then running FindHBond or its command works, at least for me.
> 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 Nov 20, 2015, at 5:29 PM, George Green <soyo.green at gmail.com> wrote:
> > 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. :)
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