[Chimera-users] Monitoring hbonds in chimera

Neha Gandhi n.gandhiau at gmail.com
Fri Jun 28 02:52:25 PDT 2013

Dear Users,

I am trying to use hbond command in the movie tool of Chimera 1.8. I want
to repeat hbond analyses with different criteria simultaneously in a single

these are my commands

select :9 at O1P,O2P,O3P,N,H :12 at N,H
findhbond selRestrictboth linewidth 2 color green reveal true (..I want to
monitor hydrogen bond between these two residues with default criteria)
select :3 at O1P,O2P,O3P :6 at O1P,O2P
findhbond selRestrict any color black reveal true relax true distSlop 2.7
intraRes false

When I tried these commands in one single script, I could see hydrogen
bonds displayed for residue 3 and 6 and not between residues 9 and 12.

Hopefully you can correct me. Your help is appreciated

Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Research Gate
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