Dear Elaine: Thank you very much for your instruction. We'll follow your guide. Best wishes WU Xue

From: Elaine Meng <meng@cgl.ucsf.edu> Reply-To: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> To: 吴雪<wuxue@nankai.edu.cn> Subject: Re: [Chimera-users] question about Chimera Date: Tue, 22 Sep 2009 11:00:11 -0700

Dear Wu Xue, There are several different distance and angle cutoffs that depend on the donor and acceptor atom types. For example, the distance and angle cutoffs for finding a H-bond donated from hydroxyl -OH to carbonyl =O will be different than from amine -NH3 to carbonyl =O. The cutoff values are taken from tables in this paper:

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.

As discussed in the FindHBond documentation,

findhbond.html#criteria>

the criteria in this paper were based on very high resolution crystal structures of small molecules. Typically the structures in the PDB are not so high resolution and so the criteria are relaxed. For example, if a strict criterion from the paper is 2.8 Angstroms cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms. We set the default relaxation amounts to what we felt gives reasonable results on most PDB structures. However, we made them user-adjustable so that if you don't like them, you can change the values to whatever you want.

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 Sep 22, 2009, at 4:18 AM, 吴雪 wrote:

...

Dear colleague: I have a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond. If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction? Sincerly Yours WU Xue