[Chimera-users] Monitoring hbonds in chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 28 10:25:26 PDT 2013


Dear Dr. Gandhi,
The second findhbond command will erase the previous H-bonds (from the first findhbond command) unless you use the "retainCurrent true" option in the second findhbond command.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html#options>

Another problem I can see is that there should be a space between "selRestrict" and "both".  Other possible reasons for no Hbond to be shown are:
(a) the atoms do not meet the criteria (for example, they are too far apart)
(b) your select command didn't select the atoms (for example, if their names didn't match what was in your command)

You can the commands by entering them into the command line before putting them into a script.  If the residues are already displayed, you do not need "reveal true"

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 Jun 28, 2013, at 2:52 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:

> 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 script
> 
> 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)
> ~sel
> select :3 at O1P,O2P,O3P :6 at O1P,O2P
> findhbond selRestrict any color black reveal true relax true distSlop 2.7 intraRes false
> ~sel
> 
> 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 
> -- 
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia







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