
Dear Support Team, Thanks for the academic free of Chimera. I have a doubt, how can I visualize H-bonding interactions of docked structure of protein-protein interaction. I used FireDock for docking studies. While running on FindHbond on structure/binding tool it says no H-bonds, but i click both shows something.....How can i see protein-protein interacting HBond and label it? For the reference, I enclosed two files. Thanks in advance! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China

Dear Dr. Selvaraj, I CC’d chimera-users@cgl.ucsf.edu (this is the best address for Chimera questions). I don’t know where you are seeing “no H-bonds” because I didn’t have that problem. If I start Chimera, open your two files, and choose menu: Tools… Surface/Binding Analysis… FindHBond, and click “Apply” on that dialog (or “OK” which is the same, except it also makes the dialog disappear), it says in the Reply Log that there are 629 H-bonds found. (open Reply Log from Favorites menu) Many orange lines are drawn on the structure to show the H-bonds. If you want to label the H-bonds with distance, check the “Label H-bond with distance” option before clicking Apply. If you want to make sure all the H-bonds are shown, check the option “If endpoint atom hidden, show endpoint residue”. If you only want the H-bonds between the two proteins, not the ones within each protein, check the “inter-model” option near the top right of the dialog. With that option, Reply Log says that 312 hydrogen bonds are found. There are also options to write all the information (atom names, distances etc.) to the Log and/or to an output text file. I hope this helps, ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2017, at 5:52 PM, Gurudeeban Selvaraj <gurudeeb99@qq.com> wrote:
Dear Support Team, Thanks for the academic free of Chimera. I have a doubt, how can I visualize H-bonding interactions of docked structure of protein-protein interaction. I used FireDock for docking studies. While running on FindHbond on structure/binding tool it says no H-bonds, but i click both shows something.....How can i see protein-protein interacting HBond and label it?
For the reference, I enclosed two files.
Thanks in advance! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher

On Sep 28, 2017, at 1:54 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Many orange lines are drawn on the structure to show the H-bonds.
One minor correction: for you, the lines will be whatever color is shown in the square color well near the top of the H-bond dialog… the default is a bright blue color similar to cyan. Elaine
participants (2)
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Elaine Meng
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Gurudeeban Selvaraj